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Nesvilab / FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
http://fragpipe.nesvilab.org
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Protein grouping for sample digested with multiple proteases #1052

Closed TeckYewLow closed 1 year ago

TeckYewLow commented 1 year ago

Hi,

I am analyzing a sample that has been digested with 5 different proteases, i.e. Trypsin, LysC, AspN, GluC and Chymotrypsin. I am planning to analyze these data with MSFragger and finally end up with only one protein.tsv to improve protein coverage, I cannot seem to figure out how to do it in MSfragger. Presumably, I plan to load all my mzML files, then configure the Workflow tab in away that groups of mzML that were produced by the same protease were assigned the same MSFragger parameters (Enzymes, Fragmentation method, mass tolerance etc). Then protein grouping is performed on these different enzymatic digets.

Please advise me how we can do it.

Best,

Teck

fcyu commented 1 year ago

Hi Teck,

FragPipe does not support the "parameter group". Therefore, FragPipe can't analyze your data in one job fully automatically. But you can first run MSFragger (inside FragPipe) 5 times corresponding to 5 enzymes. Each search writes the result files to a folder, say exp_N, where N is one of 1 to 5. Let assume that your folders are organized as follows

top_result_folder
|_______exp_1
|_______exp_2
|_______exp_3
|_______exp_4
|_______exp_5

After all MSFragger job finishes, load all of your mzML files, assign them to experiment exp_1 ... exp_5, load the LFQ-MBR workflow, uncheck/disable MSFragger, set the result folder to top_result_folder, and click Run. Theoretically, it should work. But I didn't test this idea. Could you have a try and let me know if it works?

Thanks,

Fengchao

TeckYewLow commented 1 year ago

Thanks! Good idea to work around!

Best regards,

Teck Yew

On Sat, Mar 25, 2023 at 11:11 AM Fengchao @.***> wrote:

Hi Teck,

FragPipe does not support the "parameter group". Therefore, FragPipe can't analyze your data in one job fully automatically. But you can first run MSFragger (inside FragPipe) 5 times corresponding to 5 enzymes. Each search writes the result files to a folder, say exp_N, where N is one of 1 to 5. Let assume that your folders are organized as follows

top_result_folder|___exp_1|___exp_2|___exp_3|___exp_4|___exp_5

After all MSFragger job finishes, load all of your mzML files, assign them to experiment exp_1 ... exp_5, load the LFQ-MBR workflow, uncheck/disable MSFragger, set the result folder to top_result_folder, and click Run. Theoretically, it should work. But I didn't test this idea. Could you have a try and let me know if it works?

Thanks,

Fengchao

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anesvi commented 1 year ago

Teck, let us know if it work, and we can write a short tutorial for the website. I think others would want to know if too. Thanks, Alexey

TeckYewLow commented 1 year ago

Sure, Alexey!

Low Teck Yew, PhD Associate Professor /Senior Research Fellow Secretary-General, Asia Oceania Human Proteome Organisation (AOHUPO) UKM Medical Molecular Biology Institute (UMBI) UKM Medical Center Universiti Kebangsaan Malaysia Jalan Yaacob Latiff Bandar Tun Razak, 56000 Cheras Kuala Lumpur E-mail: @.*** Web: http://www.ukm.my/umbi

https://www.aohupo-aoapo-2023.org/

On Sat, 25 Mar 2023 at 22:04, Alexey Nesvizhskii @.***> wrote:

Teck, let us know if it work, and we can write a short tutorial for the website. I think others would want to know if too. Thanks, Alexey

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TeckYewLow commented 1 year ago

I have tried. It seems to work. But I have tried only with small sample size.

(i) Basically, I created a common output directory called OUTPUT as a parental folder at the RUN tab. (ii) Then I modify the parameters in MSFRAGGER tab accordingly, and make sure the right FASTA is loaded. (iii) For the first MS dataset (TRYPSIN), I load all mzML files into the WORKFLOW tab and give a common EXPERIMENT name such as TRYPSIN, and click run. (iv) When the run finishes, I get some result files generated inside a TRYPSIN folder, which is in turn located inside the OUTPUT folder. There were some other files such as combined.prot.xml; filelist_proteinprophet.txt; fragpipe-files.fp-manifest etc inside the OUPUT folder but not inside the TRYPSIN subfolder. (v) Then for the second dataset (CHYMOTRYPSIN), I repeated step (iii). >> My question is: when I click run, I was asked about whether to delete the existing combined.prot.xml. I ignored and continued. Does that affect my final combined results? (vi) When the CHYMOTRYPSIN run finished. I tried to combine both TRYPSIN and CHYMOTRPSIN together as a single report. So I loaded all the mzML files for TRYPSIN and CHYMOTRYPSIN back into the WORKFLOW tab, and named these datasets as TRYPSIN and CHYMOTRYPSIN respectively. (vii) Then I disabled the MSFRAGGER tab, but left the VALIDATION tab in the previous setting. (viii) This time, I additionally selected the MS1 QUANT tab, and next selected ION QUANT. (ix) Finally I got a report that combined both TRYPSIN and CHYMOTRYPSIN datasets. I can also view both TRYPSIN and CHYMOTRYPSIN MS2 spectra with the PDV-Viewer.

fcyu commented 1 year ago

Hi @TeckYewLow ,

For the individual runs, you only need to run MSFragger but disable/uncheck other steps (e.g., validation, MS1 quant).

My question is: when I click run, I was asked about whether to delete the existing combined.prot.xml. I ignored and continued. Does that affect my final combined results?

It should not affect the result because the combined.prot.xml files will be overwritten by your last/combined run.

If you are not sure, you can share some log files with us.

Best,

Fengchao

TeckYewLow commented 1 year ago

Hi @fcyu

Thanks I will try!

TeckYewLow commented 1 year ago

Hi @fcyu

I tried with a much bigger dataset. I disabled MSFragger but only ran Validation and LFQ-MBR. An error happened at MSBooster which prevented further processing.

"Edited pin file at C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN_edited.pin Processing TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzML umich.ms.fileio.exceptions.FileParsingException: java.util.concurrent.TimeoutException at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:198) at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:807) at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:791) at Features.mzMLReader.(mzMLReader.java:72) at Features.percolatorFormatter.editPin(percolatorFormatter.java:322) at Features.MainClass.main(MainClass.java:588) Caused by: java.util.concurrent.TimeoutException at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:204) at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:191) ... 5 more Process 'MSBooster' finished, exit code: 1 Process returned non-zero exit code, stopping_

Cancelling 1075 remaining tasks

Subsequently, I also disabled MSBooster. The errors happened again at Percolator.

"java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar com.github.chhh.utils.FileDelete C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: C:\Fragpipe_19.2\Results\RAT_COMBINED\BnLyscTT] java -cp C:\Fragpipe_19.2\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC.pin TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC_percolator_target_psms.tsv TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC_percolator_decoy_psms.tsv interact-TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC DDA 0.5 J:\X10_Rat_Proteogenomics_01\02_mzML_files\05_BN_LysC_TTOF_WIFF\TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar com.github.chhh.utils.FileDelete C:\Fragpipe_19.2\Results\RAT_COMBINED\BnLyscTT\TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar com.github.chhh.utils.FileDelete C:\Fragpipe_19.2\Results\RAT_COMBINED\BnLyscTT\TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT] java -cp C:\Fragpipe_19.2\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.pin TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN_percolator_target_psms.tsv TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN_percolator_decoy_psms.tsv interact-TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN DDA 0.5 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzML Exception in thread "main" java.lang.NullPointerException at com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML.percolatorToPepXML(PercolatorOutputToPepXML.java:310) at com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML.main(PercolatorOutputToPepXML.java:59) Process 'Percolator: Convert to pepxml' finished, exit code: 1 Process returned non-zero exit code, stopping


Cancelling 577 remaining tasks"
danielgeiszler commented 1 year ago

Did you ever run MSFragger on the much bigger dataset, or did you skip to validation and LFQ-MBR without running MSFragger on the bigger dataset?

On Wed, Mar 29, 2023 at 13:46 TeckYewLow @.***> wrote:

Hi @fcyu https://github.com/fcyu

I tried with a much bigger dataset. I disabled MSFragger but only ran Validation and LFQ-MBR. An error happened at MSBooster which prevented further processing.

"Edited pin file at C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN_edited.pin Processing TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzML umich.ms.fileio.exceptions.FileParsingException: java.util.concurrent.TimeoutException at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:198) at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:807) at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:791) at Features.mzMLReader.(mzMLReader.java:72) at Features.percolatorFormatter.editPin(percolatorFormatter.java:322) at Features.MainClass.main(MainClass.java:588) Caused by: java.util.concurrent.TimeoutException at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:204) at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:191) ... 5 more Process 'MSBooster' finished, exit code: 1 Process returned non-zero exit code, stopping_

Cancelling 1075 remaining tasks

Subsequently, I also disabled MSBooster. The errors happened again at Percolator.

"java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar com.github.chhh.utils.FileDelete C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: C:\Fragpipe_19.2\Results\RAT_COMBINED\BnLyscTT] java -cp C:\Fragpipe_19.2\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC.pin TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC_percolator_target_psms.tsv TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC_percolator_decoy_psms.tsv interact-TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC DDA 0.5 J:\X10_Rat_Proteogenomics_01\02_mzML_files\05_BN_LysC_TTOF_WIFF\TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar com.github.chhh.utils.FileDelete C:\Fragpipe_19.2\Results\RAT_COMBINED\BnLyscTT\TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar com.github.chhh.utils.FileDelete C:\Fragpipe_19.2\Results\RAT_COMBINED\BnLyscTT\TT1_111130_TY_BN3_LysC_SCX_20percent_F31_recal_371_445-BN3_LysC_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT] java -cp C:\Fragpipe_19.2\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.pin TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN_percolator_target_psms.tsv TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN_percolator_decoy_psms.tsv interact-TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN DDA 0.5 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzML Exception in thread "main" java.lang.NullPointerException at com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML.percolatorToPepXML(PercolatorOutputToPepXML.java:310) at com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML.main(PercolatorOutputToPepXML.java:59) Process 'Percolator: Convert to pepxml' finished, exit code: 1 Process returned non-zero exit code, stopping

Cancelling 577 remaining tasks"

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TeckYewLow commented 1 year ago

As mentioned in my earlier post, this is what I did (after some modification):

(i) I created a common output directory called OUTPUT as a parental folder at the RUN tab. (ii) Then I modify the parameters in MSFRAGGER tab accordingly, and make sure the right FASTA is loaded. I disabled Validation and LFQ-MBR at this stage. (iii) For the first MS dataset (TRYPSIN), I load all mzML files into the WORKFLOW tab and give a common EXPERIMENT name such as TRYPSIN, and click run. (iv) When the run finishes, I get some result files generated inside a TRYPSIN folder, which is in turn located inside the OUTPUT folder. (v) Then for the second dataset (CHYMOTRYPSIN) an other datasets, I repeated step (iii). (vi) When the CHYMOTRYPSIN run finished. I tried to combine both TRYPSIN and CHYMOTRPSIN together as a single report. So I loaded all the mzML files for TRYPSIN and CHYMOTRYPSIN back into the WORKFLOW tab, and named these datasets as TRYPSIN and CHYMOTRYPSIN respectively. (vii) Then I disabled the MSFRAGGER tab, but selected the VALIDATION tab in the previous setting. (viii) This time, I additionally selected the MS1 QUANT tab, and next selected ION QUANT.

danielgeiszler commented 1 year ago

The issue seems to be with the following file or dataset not being found. Can you please upload the log for where you processed this file with MSFragger?

RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN

TeckYewLow commented 1 year ago

Hi Daniel,

This is the log related to the sample you mentioned:

System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.17, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation .NET Core Info: N/A

Version info: FragPipe version 19.2-build28 MSFragger version 3.7 IonQuant version 1.8.10 Philosopher version 5.0.0-RC14

LCMS files: Experiment/Group: BnAspnTT

54 commands to execute: CheckCentroid java -Xmx6G -cp "C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;C:\Fragpipe_19.2\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.mzML 10 MSFragger [Work dir: C:\Fragpipe_19.2\Results\RAT_COMBINED] java -jar -Dfile.encoding=UTF-8 -Xmx6G C:\Fragpipe_19.2\tools\MSFragger-3.7\MSFragger-3.7.jar C:\Fragpipe_19.2\Results\RAT_COMBINED\fragger.params J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.mzML MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.pin MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.pepXML MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.pin


Execution order:

    Cmd: [START], Work dir: [C:\Fragpipe_19.2\Results\RAT_COMBINED]
    Cmd: [CheckCentroid], Work dir: [C:\Fragpipe_19.2\Results\RAT_COMBINED]
    Cmd: [MSFragger], Work dir: [C:\Fragpipe_19.2\Results\RAT_COMBINED]

>rev_sp|A0A096MJN4|SEPT4_RAT Septin-4 OS=Rattus norvegicus OX=10116 GN=Septin4 PE=1 SV=1
>rev_tr|II_2634997|Megf11_RAT XM_017596055 OS=Rattus norvegicus OX=10116 OS GN=Megf11 PE=0 SV=0
>rev_tr|IP_1283565|Tdp1_RAT NM_001031657 XM_006240432 ENSRNOT00000005167 OS=Rattus norvegicus OX=10116 OS GN=Tdp1 PE=0 SV=0
>rev_tr|IP_1316095|Eif4g1,AC094053.1,LOC100911693,LOC682402_RAT XM_006248583 XM_017598182 ENSRNOT00000042983 XM_017598184 XM_006248584 ENSRNOT00000041777 XM_006248585 XM_008768835 ENSRNOT00000040029 XR_590992 XM_017591374 XM_006248581 XM_017598183 OS=Rattus norvegicus OX=10116 OS GN=Eif4g1,AC094053.1,LOC100911693,LOC682402 PE=0 SV=0
>rev_tr|IP_1349058|AC131360.1,Pcdhb17_RAT ENSRNOT00000060486 XM_017601100 OS=Rattus norvegicus OX=10116 OS GN=AC131360.1,Pcdhb17 PE=0 SV=0
>rev_tr|IP_1381515|AABR07030793.2_RAT ENSRNOT00000081753 OS=Rattus norvegicus OX=10116 OS GN=AABR07030793.2 PE=0 SV=0
>rev_tr|IP_2584976|Ints1_RAT XM_008769039 OS=Rattus norvegicus OX=10116 OS GN=Ints1 PE=0 SV=0
>rev_tr|IP_2617038|LOC108350039_RAT XR_001836771 OS=Rattus norvegicus OX=10116 OS GN=LOC108350039 PE=0 SV=0
>rev_tr|IP_2648693|Akap2_RAT NM_001309260 NM_001011974 XM_006238186 XM_006238185 OS=Rattus norvegicus OX=10116 OS GN=Akap2 PE=0 SV=0
>rev_tr|IP_2681410|Sptbn1_RAT XM_008770458 OS=Rattus norvegicus OX=10116 OS GN=Sptbn1 PE=0 SV=0
>rev_tr|Q9WVL9|Q9WVL9_RAT Natural killer cell granule protein 7 OS=Rattus norvegicus OX=10116 GN=Nkg7 PE=2 SV=1
>tr|II_2634758|Kif23_RAT XM_017595657 NM_001108155 OS=Rattus norvegicus OX=10116 OS GN=Kif23 PE=0 SV=0
>tr|IP_1283556|Psmc1_RAT ENSRNOT00000005329 OS=Rattus norvegicus OX=10116 OS GN=Psmc1 PE=0 SV=0
>tr|IP_1316087|AABR07009600.1_RAT ENSRNOT00000086516 OS=Rattus norvegicus OX=10116 OS GN=AABR07009600.1 PE=0 SV=0
>tr|IP_1349049|LOC108348772,AABR07031740.1_RAT XR_001842089 ENSRNOT00000089581 OS=Rattus norvegicus OX=10116 OS GN=LOC108348772,AABR07031740.1 PE=0 SV=0
>tr|IP_1381507|Foxj1,AABR07030823.1_RAT ENSRNOT00000072687 NM_053832 OS=Rattus norvegicus OX=10116 OS GN=Foxj1,AABR07030823.1 PE=0 SV=0
>tr|IP_2584967|Mad1l1_RAT XM_017598453 OS=Rattus norvegicus OX=10116 OS GN=Mad1l1 PE=0 SV=0
>tr|IP_2617030|LOC102547484_RAT XR_591145 OS=Rattus norvegicus OX=10116 OS GN=LOC102547484 PE=0 SV=0
>tr|IP_2648684|Ptpn3_RAT XM_008763739 OS=Rattus norvegicus OX=10116 OS GN=Ptpn3 PE=0 SV=0
>tr|IP_2681398|Gpr75_RAT XM_006251616 OS=Rattus norvegicus OX=10116 OS GN=Gpr75 PE=0 SV=0
>tr|Q9R005|Q9R005_RAT Prolactin family 7, subfamily d, member 1 OS=Rattus norvegicus OX=10116 GN=Prl7d1 PE=2 SV=1
# FragPipe v19.2-build28ui state cache

# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=C\:\\Fragpipe_19.2\\tools\\fasta\\RAT\\2023-03-29-decoys-contam-Rat_ENSEMBL_OpenProtPredicted_Combined_20230327.FASTA.fas

crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.library=
diann.q-value=0.01
diann.quantification-strategy=3
diann.run-dia-nn=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=true
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fragpipe-config.bin-ionquant=C\:\\MSFRAGGER\\fragpipe\\tools\\IonQuant-1.8.10.jar
fragpipe-config.bin-msfragger=C\:\\Fragpipe_19.2\\tools\\MSFragger-3.7\\MSFragger-3.7.jar
fragpipe-config.bin-philosopher=C\:\\Fragpipe_19.2\\tools\\philosopher-v5.0.0-RC14.exe
fragpipe-config.bin-python=C\:\\MSFRAGGER\\Anaconda\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=true
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage_1=3
msfragger.allowed_missed_cleavage_2=3
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=0.1
msfragger.fragment_mass_units=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=custom
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-50
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=50
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=DE
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=aspnDE
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=N
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,KR,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mzml=false
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=ETD
opair.glyco_db=
opair.max_glycans=4
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=false
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=00.2
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=00.1
ptmshepherd.diagmine_fragMinSpecDiff=00.1
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=00.2
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.prob_dhexOx=2,0.5,0.1
ptmshepherd.prob_dhexY=2,0.5
ptmshepherd.prob_neuacOx=2,0.05,0.2
ptmshepherd.prob_neugcOx=2,0.05,0.2
ptmshepherd.prob_phosphoOx=2,0.05,0.2
ptmshepherd.prob_regY=5,0.5
ptmshepherd.prob_sulfoOx=2,0.05,0.2
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=false
run-psm-validation=true
run-validation-tab=false
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=false
saintexpress.virtual-controls=100
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.fragment.a=false
speclibgen.easypqp.fragment.b=true
speclibgen.easypqp.fragment.c=false
speclibgen.easypqp.fragment.x=false
speclibgen.easypqp.fragment.y=true
speclibgen.easypqp.fragment.z=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
sub_mzml_prob_threshold=0
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=C\:\\Fragpipe_19.2\\Results\\RAT_COMBINED
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=6
workflow.threads=10

CheckCentroid java -Xmx6G -cp "C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;C:\Fragpipe_19.2\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.mzML 10 Done in 11988 ms. Process 'CheckCentroid' finished, exit code: 0 MSFragger [Work dir: C:\Fragpipe_19.2\Results\RAT_COMBINED] java -jar -Dfile.encoding=UTF-8 -Xmx6G C:\Fragpipe_19.2\tools\MSFragger-3.7\MSFragger-3.7.jar C:\Fragpipe_19.2\Results\RAT_COMBINED\fragger.params J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.mzML J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.mzML MSFragger version MSFragger-3.7 Batmass-IO version 1.28.9 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.17, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 6 GB memory Checking database... Unknown parameters: write_mzbin_all = 0 Checking spectral files... J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.mzML: Scans = 33994 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.mzML: Scans = 34624 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.mzML: Scans = 34970 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.mzML: Scans = 37655 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.mzML: Scans = 35039 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.mzML: Scans = 37987 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.mzML: Scans = 40409 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.mzML: Scans = 44207 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.mzML: Scans = 45692 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.mzML: Scans = 27642 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.mzML: Scans = 32292 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.mzML: Scans = 38369 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.mzML: Scans = 42166 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.mzML: Scans = 40700 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.mzML: Scans = 41103 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.mzML: Scans = 46474 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzML: Scans = 40223 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.mzML: Scans = 24007 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.mzML: Scans = 14273 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.mzML: Scans = 34444 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.mzML: Scans = 42565 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.mzML: Scans = 47772 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.mzML: Scans = 32518 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.mzML: Scans = 45764 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.mzML: Scans = 36123 J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.mzML: Scans = 47185 ***FIRST SEARCH**** Parameters: num_threads = 10 database_name = C:\Fragpipe_19.2\tools\fasta\RAT\2023-03-29-decoys-contam-Rat_ENSEMBL_OpenProtPredicted_Combined_20230327.FASTA.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 100.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mzml = 0 write_uncalibrated_mgf = false isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = aspnDE search_enzyme_sense_1 = N search_enzyme_cut_1 = DE search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 activation_types = all remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 489897 of length 8: 471025 of length 9: 453886 of length 10: 446056 of length 11: 431908 of length 12: 407777 of length 13: 390157 of length 14: 382836 of length 15: 359229 of length 16: 343808 of length 17: 325786 of length 18: 313447 of length 19: 294845 of length 20: 277656 of length 21: 269994 of length 22: 250568 of length 23: 235770 of length 24: 227678 of length 25: 212971 of length 26: 202376 of length 27: 191385 of length 28: 208130 of length 29: 195960 of length 30: 185162 of length 31: 170265 of length 32: 160280 of length 33: 148027 of length 34: 138614 of length 35: 127917 of length 36: 119336 of length 37: 111684 of length 38: 102339 of length 39: 96554 of length 40: 88472 of length 41: 82765 of length 42: 70904 of length 43: 59142 of length 44: 45528 of length 45: 31839 of length 46: 19968 of length 47: 11212 of length 48: 6299 of length 49: 2937 of length 50: 1465 In total 9163854 peptides. Generated 18672720 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.50 Da. 826617050 fragments to be searched in 4 slices (12.32 GB total) Operating on slice 1 of 4: Fragment index slice generated in 3.06 s

  1. TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.mzML 7.7 s | deisotoping 0.5 s [progress: 12726/12726 (100%) - 4543 spectra/s] 2.8s
  2. TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.mzML 8.2 s | deisotoping 0.5 s [progress: 33311/33311 (100%) - 6261 spectra/s] 5.3s
  3. TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.mzML 7.8 s | deisotoping 0.5 s [progress: 35323/35323 (100%) - 6625 spectra/s] 5.3s
  4. TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.mzML 7.2 s | deisotoping 0.3 s [progress: 34519/34519 (100%) - 8063 spectra/s] 4.3s
  5. TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.mzML 8.6 s | deisotoping 0.6 s [progress: 32939/32939 (100%) - 6446 spectra/s] 5.1s
  6. TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.mzML 6.4 s | deisotoping 0.3 s [progress: 30698/30698 (100%) - 8601 spectra/s] 3.6s
  7. TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.mzML 6.3 s | deisotoping 0.1 s [progress: 21622/21622 (100%) - 11303 spectra/s] 1.9s
  8. TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.mzML 9.3 s | deisotoping 0.3 s [progress: 20679/20679 (100%) - 7253 spectra/s] 2.9s
  9. TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.mzML 8.3 s | deisotoping 0.8 s [progress: 31617/31617 (100%) - 5817 spectra/s] 5.4s
  10. TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.mzML 7.1 s | deisotoping 0.7 s [progress: 28464/28464 (100%) - 6241 spectra/s] 4.6s
  11. TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.mzML 8.7 s | deisotoping 0.7 s [progress: 39642/39642 (100%) - 6454 spectra/s] 6.1s
  12. TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.mzML 8.7 s | deisotoping 0.7 s [progress: 41586/41586 (100%) - 6598 spectra/s] 6.3s
  13. TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.mzML 8.8 s | deisotoping 0.6 s [progress: 42884/42884 (100%) - 7830 spectra/s] 5.5s
  14. TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.mzML 8.7 s | deisotoping 0.4 s [progress: 40995/40995 (100%) - 8174 spectra/s] 5.0s
  15. TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.mzML 8.6 s | deisotoping 0.3 s [progress: 37885/37885 (100%) - 10600 spectra/s] 3.6s
  16. TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.mzML 9.1 s | deisotoping 0.6 s [progress: 28201/28201 (100%) - 7064 spectra/s] 4.0s
  17. TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.mzML 12.2 s | deisotoping 0.8 s [progress: 34746/34746 (100%) - 5863 spectra/s] 5.9s
  18. TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.mzML 9.8 s | deisotoping 0.9 s [progress: 37714/37714 (100%) - 6566 spectra/s] 5.7s
  19. TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.mzML 11.6 s | deisotoping 0.7 s [progress: 37336/37336 (100%) - 6749 spectra/s] 5.5s
  20. TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.mzML 9.5 s | deisotoping 0.8 s [progress: 38324/38324 (100%) - 7023 spectra/s] 5.5s
  21. TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.mzML 12.5 s | deisotoping 0.7 s [progress: 44050/44050 (100%) - 7933 spectra/s] 5.6s
  22. TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.mzML 10.5 s | deisotoping 0.8 s [progress: 42991/42991 (100%) - 7196 spectra/s] 6.0s
  23. TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzML 12.8 s | deisotoping 0.9 s [progress: 36700/36700 (100%) - 6415 spectra/s] 5.7s
  24. TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.mzML 10.3 s | deisotoping 1.0 s [progress: 30550/30550 (100%) - 5618 spectra/s] 5.4s
  25. TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.mzML 9.7 s | deisotoping 0.6 s [progress: 31912/31912 (100%) - 7103 spectra/s] 4.5s
  26. TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.mzML 8.1 s | deisotoping 0.3 s [progress: 36336/36336 (100%) - 7954 spectra/s] 4.6s Operating on slice 2 of 4: Fragment index slice generated in 3.06 s
  27. TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.mzML 7.0 s | deisotoping 0.1 s [progress: 12726/12726 (100%) - 18390 spectra/s] 0.7s
  28. TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.mzML 7.8 s | deisotoping 0.5 s [progress: 33311/33311 (100%) - 15301 spectra/s] 2.2s
  29. TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.mzML 7.5 s | deisotoping 0.5 s [progress: 35323/35323 (100%) - 17023 spectra/s] 2.1s
  30. TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.mzML 9.1 s | deisotoping 0.4 s [progress: 34519/34519 (100%) - 20908 spectra/s] 1.7s
  31. TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.mzML 7.7 s | deisotoping 0.6 s [progress: 32939/32939 (100%) - 16611 spectra/s] 2.0s
  32. TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.mzML 6.4 s | deisotoping 0.3 s [progress: 30698/30698 (100%) - 22213 spectra/s] 1.4s
  33. TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.mzML 6.3 s | deisotoping 0.1 s [progress: 21622/21622 (100%) - 31246 spectra/s] 0.7s
  34. TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.mzML 7.0 s | deisotoping 0.4 s [progress: 20679/20679 (100%) - 13428 spectra/s] 1.5s
  35. TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.mzML 8.3 s | deisotoping 0.8 s [progress: 31617/31617 (100%) - 12274 spectra/s] 2.6s
  36. TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.mzML 7.2 s | deisotoping 0.7 s [progress: 28464/28464 (100%) - 13932 spectra/s] 2.0s
  37. TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.mzML 8.6 s | deisotoping 0.7 s [progress: 39642/39642 (100%) - 16108 spectra/s] 2.5s
  38. TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.mzML 8.7 s | deisotoping 0.7 s [progress: 41586/41586 (100%) - 19469 spectra/s] 2.1s
  39. TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.mzML 10.9 s | deisotoping 0.6 s [progress: 42884/42884 (100%) - 24228 spectra/s] 1.8s
  40. TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.mzML 8.8 s | deisotoping 0.5 s [progress: 40995/40995 (100%) - 27513 spectra/s] 1.5s
  41. TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.mzML 8.5 s | deisotoping 0.3 s [progress: 37885/37885 (100%) - 33796 spectra/s] 1.1s
  42. TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.mzML 10.4 s | deisotoping 0.6 s [progress: 28201/28201 (100%) - 14440 spectra/s] 2.0s
  43. TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.mzML 10.2 s | deisotoping 0.8 s [progress: 34746/34746 (100%) - 14130 spectra/s] 2.5s
  44. TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.mzML 10.0 s | deisotoping 0.9 s [progress: 37714/37714 (100%) - 17976 spectra/s] 2.1s
  45. TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.mzML 11.8 s | deisotoping 0.7 s [progress: 37336/37336 (100%) - 19702 spectra/s] 1.9s
  46. TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.mzML 9.5 s | deisotoping 0.7 s [progress: 38324/38324 (100%) - 22307 spectra/s] 1.7s
  47. TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.mzML 10.6 s | deisotoping 0.7 s [progress: 44050/44050 (100%) - 21732 spectra/s] 2.0s
  48. TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.mzML 10.6 s | deisotoping 0.8 s [progress: 42991/42991 (100%) - 19330 spectra/s] 2.2s
  49. TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzML 10.5 s | deisotoping 0.9 s [progress: 36700/36700 (100%) - 16399 spectra/s] 2.2s
  50. TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.mzML 10.9 s | deisotoping 1.0 s [progress: 30550/30550 (100%) - 14541 spectra/s] 2.1s
  51. TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.mzML 9.4 s | deisotoping 0.7 s [progress: 31912/31912 (100%) - 18152 spectra/s] 1.8s
  52. TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.mzML 10.0 s | deisotoping 0.4 s [progress: 36336/36336 (100%) - 21101 spectra/s] 1.7s Operating on slice 3 of 4: Fragment index slice generated in 2.65 s
  53. TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.mzML 7.3 s | deisotoping 0.1 s [progress: 12726/12726 (100%) - 29873 spectra/s] 0.4s
  54. TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.mzML 7.8 s | deisotoping 0.5 s [progress: 33311/33311 (100%) - 28766 spectra/s] 1.2s
  55. TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.mzML 8.1 s | deisotoping 0.5 s [progress: 35323/35323 (100%) - 34195 spectra/s] 1.0s
  56. TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.mzML 7.0 s | deisotoping 0.3 s [progress: 34519/34519 (100%) - 38269 spectra/s] 0.9s
  57. TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.mzML 7.5 s | deisotoping 0.6 s [progress: 32939/32939 (100%) - 30109 spectra/s] 1.1s
  58. TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.mzML 6.4 s | deisotoping 0.3 s [progress: 30698/30698 (100%) - 46796 spectra/s] 0.7s
  59. TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.mzML 8.1 s | deisotoping 0.1 s [progress: 21622/21622 (100%) - 51116 spectra/s] 0.4s
  60. TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.mzML 7.0 s | deisotoping 0.3 s [progress: 20679/20679 (100%) - 19290 spectra/s] 1.1s
  61. TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.mzML 8.4 s | deisotoping 0.8 s [progress: 31617/31617 (100%) - 23061 spectra/s] 1.4s
  62. TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.mzML 7.2 s | deisotoping 0.7 s [progress: 28464/28464 (100%) - 26429 spectra/s] 1.1s
  63. TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.mzML 10.8 s | deisotoping 0.6 s [progress: 39642/39642 (100%) - 26358 spectra/s] 1.5s
  64. TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.mzML 8.7 s | deisotoping 0.6 s [progress: 41586/41586 (100%) - 35696 spectra/s] 1.2s
  65. TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.mzML 8.9 s | deisotoping 0.5 s [progress: 42884/42884 (100%) - 41354 spectra/s] 1.0s
  66. TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.mzML 10.8 s | deisotoping 0.5 s [progress: 40995/40995 (100%) - 47613 spectra/s] 0.9s
  67. TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.mzML 8.6 s | deisotoping 0.3 s [progress: 37885/37885 (100%) - 50716 spectra/s] 0.7s
  68. TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.mzML 9.2 s | deisotoping 0.5 s [progress: 28201/28201 (100%) - 22400 spectra/s] 1.3s
  69. TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.mzML 12.3 s | deisotoping 0.8 s [progress: 34746/34746 (100%) - 23605 spectra/s] 1.5s
  70. TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.mzML 10.0 s | deisotoping 0.9 s [progress: 37714/37714 (100%) - 29487 spectra/s] 1.3s
  71. TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.mzML 9.5 s | deisotoping 0.7 s [progress: 37336/37336 (100%) - 32186 spectra/s] 1.2s
  72. TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.mzML 9.6 s | deisotoping 0.7 s [progress: 38324/38324 (100%) - 35783 spectra/s] 1.1s
  73. TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.mzML 10.1 s | deisotoping 0.7 s [progress: 44050/44050 (100%) - 37394 spectra/s] 1.2s
  74. TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.mzML 12.1 s | deisotoping 0.7 s [progress: 42991/42991 (100%) - 34012 spectra/s] 1.3s
  75. TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzML 10.5 s | deisotoping 0.9 s [progress: 36700/36700 (100%) - 28989 spectra/s] 1.3s
  76. TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.mzML 10.4 s | deisotoping 1.0 s [progress: 30550/30550 (100%) - 24150 spectra/s] 1.3s
  77. TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.mzML 11.6 s | deisotoping 0.6 s [progress: 31912/31912 (100%) - 27846 spectra/s] 1.1s
  78. TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.mzML 7.9 s | deisotoping 0.3 s [progress: 36336/36336 (100%) - 38410 spectra/s] 0.9s Operating on slice 4 of 4: Fragment index slice generated in 3.50 s
  79. TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.mzML 6.9 s | deisotoping 0.1 s [progress: 12726/12726 (100%) - 40788 spectra/s] 0.3s | postprocessing 5.0 s
  80. TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.mzML 7.7 s | deisotoping 0.5 s [progress: 33311/33311 (100%) - 34519 spectra/s] 1.0s | postprocessing 5.2 s
  81. TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.mzML 7.8 s | deisotoping 0.5 s [progress: 35323/35323 (100%) - 35394 spectra/s] 1.0s | postprocessing 2.2 s
  82. TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.mzML 9.7 s | deisotoping 0.3 s [progress: 34519/34519 (100%) - 43149 spectra/s] 0.8s | postprocessing 1.3 s
  83. TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.mzML 7.7 s | deisotoping 0.6 s [progress: 32939/32939 (100%) - 33038 spectra/s] 1.0s | postprocessing 1.2 s
  84. TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.mzML 6.4 s | deisotoping 0.3 s [progress: 30698/30698 (100%) - 46583 spectra/s] 0.7s | postprocessing 0.8 s
  85. TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.mzML 6.4 s | deisotoping 0.1 s [progress: 21622/21622 (100%) - 49141 spectra/s] 0.4s | postprocessing 0.7 s
  86. TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.mzML 7.0 s | deisotoping 0.3 s [progress: 20679/20679 (100%) - 26176 spectra/s] 0.8s | postprocessing 0.7 s
  87. TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.mzML 8.5 s | deisotoping 0.8 s [progress: 31617/31617 (100%) - 28769 spectra/s] 1.1s | postprocessing 1.1 s
  88. TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.mzML 7.2 s | deisotoping 0.7 s [progress: 28464/28464 (100%) - 29619 spectra/s] 1.0s | postprocessing 2.0 s
  89. TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.mzML 8.8 s | deisotoping 0.8 s [progress: 39642/39642 (100%) - 31841 spectra/s] 1.2s | postprocessing 1.0 s
  90. TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.mzML 8.7 s | deisotoping 0.7 s [progress: 41586/41586 (100%) - 36383 spectra/s] 1.1s | postprocessing 0.9 s
  91. TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.mzML 10.6 s | deisotoping 0.6 s [progress: 42884/42884 (100%) - 40998 spectra/s] 1.0s | postprocessing 1.0 s
  92. TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.mzML 8.7 s | deisotoping 0.5 s [progress: 40995/40995 (100%) - 46374 spectra/s] 0.9s | postprocessing 0.9 s
  93. TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.mzML 8.6 s | deisotoping 0.3 s [progress: 37885/37885 (100%) - 51544 spectra/s] 0.7s | postprocessing 0.8 s
  94. TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.mzML 9.5 s | deisotoping 0.6 s [progress: 28201/28201 (100%) - 30687 spectra/s] 0.9s | postprocessing 0.8 s
  95. TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.mzML 10.0 s | deisotoping 0.9 s [progress: 34746/34746 (100%) - 28835 spectra/s] 1.2s | postprocessing 1.0 s
  96. TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.mzML 9.9 s | deisotoping 0.9 s [progress: 37714/37714 (100%) - 33946 spectra/s] 1.1s | postprocessing 1.3 s
  97. TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.mzML 10.0 s | deisotoping 0.7 s [progress: 37336/37336 (100%) - 35728 spectra/s] 1.0s | postprocessing 1.0 s
  98. TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.mzML 9.4 s | deisotoping 0.8 s [progress: 38324/38324 (100%) - 37244 spectra/s] 1.0s | postprocessing 0.9 s
  99. TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.mzML 12.3 s | deisotoping 0.7 s [progress: 44050/44050 (100%) - 36556 spectra/s] 1.2s | postprocessing 1.0 s
  100. TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.mzML 10.8 s | deisotoping 0.7 s [progress: 42991/42991 (100%) - 32743 spectra/s] 1.3s | postprocessing 1.0 s
  101. TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzML 10.7 s | deisotoping 0.9 s [progress: 36700/36700 (100%) - 28898 spectra/s] 1.3s | postprocessing 0.9 s
  102. TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.mzML 10.6 s | deisotoping 1.0 s [progress: 30550/30550 (100%) - 23664 spectra/s] 1.3s | postprocessing 0.9 s
  103. TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.mzML 9.3 s | deisotoping 0.7 s [progress: 31912/31912 (100%) - 30922 spectra/s] 1.0s | postprocessing 0.9 s
  104. TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.mzML 10.1 s | deisotoping 0.4 s [progress: 36336/36336 (100%) - 36889 spectra/s] 1.0s | postprocessing 0.8 s ***FIRST SEARCH DONE IN 29.324 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 2.66 2.19 0.04 0.79 6.13 8.57 -0.87 7.46
002 8.97 4.19 0.15 1.24 12.21 10.40 0.33 6.02
003 7.17 4.65 0.16 1.17 10.35 10.44 0.04 6.28
004 8.81 6.27 0.23 1.30 11.01 11.84 0.08 6.65
005 12.75 4.74 0.30 1.71 15.49 12.92 0.61 6.50
006 9.07 5.30 0.17 1.32 11.99 12.20 -0.16 7.37
007 3.19 2.65 -0.04 1.14 7.04 9.83 -1.06 8.21
008 -0.67 2.97 0.14 1.03 4.93 7.29 -0.75 7.02
009 5.83 3.30 0.10 0.95 10.53 7.80 -0.27 5.67
010 7.47 3.96 0.01 1.06 12.03 9.06 -0.28 6.02
011 3.43 2.76 0.03 1.06 7.96 7.23 -0.62 6.21
012 7.03 3.14 0.16 1.22 11.23 9.20 -0.25 6.43
013 4.91 3.15 0.05 1.10 8.90 8.95 -0.55 6.63
014 7.94 4.62 0.18 1.35 12.32 11.92 -0.33 7.50
015 4.38 2.64 0.26 1.10 9.08 8.92 -0.43 7.05
016 3.34 4.48 0.21 1.13 9.69 9.20 -0.41 6.51
017 2.04 2.71 -0.11 1.01 7.74 6.74 -0.50 6.23
018 0.68 2.60 -0.05 0.91 6.05 6.48 -0.67 6.09
019 7.06 3.48 0.14 1.19 12.60 9.57 -0.30 6.62
020 6.42 3.49 0.09 1.11 11.86 9.59 -0.36 6.57
021 6.66 4.14 0.06 1.34 12.30 10.92 -0.36 7.46
022 3.72 3.17 0.05 0.90 9.48 7.81 -0.37 6.46
023 3.83 2.89 0.04 0.95 9.62 7.88 -0.34 6.64
024 2.41 3.70 0.03 1.24 8.49 8.22 -0.41 6.31
025 5.61 4.49 0.17 1.03 11.76 10.35 -0.33 6.82
026 9.62 4.28 0.39 1.47 13.01 8.69 0.03 6.44
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count skip skip skip 10606 10721 10713 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- -------
Peaks 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- -------
Count 10757 10754 skip rest
------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 11172
------- -------
------- -------
Rm P. 0
------- -------
Count 11140
------- -------

New fragment_mass_tolerance = 20 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 9.057 MIN*****

****MAIN SEARCH**** Checking database... Unknown parameters: write_mzbin_all = 0 Parameters: num_threads = 10 database_name = C:\Fragpipe_19.2\tools\fasta\RAT\2023-03-29-decoys-contam-Rat_ENSEMBL_OpenProtPredicted_Combined_20230327.FASTA.fas decoyprefix = rev precursor_mass_lower = -50.0 precursor_mass_upper = 50.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mzml = 0 write_uncalibrated_mgf = false isotope_error = 0/1/2 mass_offsets = 0.0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = aspnDE search_enzyme_sense_1 = N search_enzyme_cut_1 = DE search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 3 num_enzyme_termini = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = true override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 activation_types = all remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 513931 of length 8: 502786 of length 9: 491206 of length 10: 490123 of length 11: 483567 of length 12: 465526 of length 13: 453361 of length 14: 452765 of length 15: 433568 of length 16: 422121 of length 17: 409740 of length 18: 401121 of length 19: 384302 of length 20: 368242 of length 21: 362835 of length 22: 342865 of length 23: 327767 of length 24: 319884 of length 25: 303401 of length 26: 292552 of length 27: 280736 of length 28: 301665 of length 29: 287007 of length 30: 275298 of length 31: 256826 of length 32: 245713 of length 33: 229410 of length 34: 217050 of length 35: 203456 of length 36: 191818 of length 37: 180524 of length 38: 168065 of length 39: 160072 of length 40: 148230 of length 41: 138745 of length 42: 122038 of length 43: 101352 of length 44: 78073 of length 45: 54370 of length 46: 33552 of length 47: 18711 of length 48: 10143 of length 49: 4761 of length 50: 2308 In total 11931586 peptides. Generated 24475672 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.10 Da. 1146153884 fragments to be searched in 5 slices (17.08 GB total) Operating on slice 1 of 5: Fragment index slice generated in 3.03 s

  1. TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.mzBIN_calibrated 0.6 s [progress: 12215/12215 (100%) - 4978 spectra/s] 2.5s
  2. TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 32345/32345 (100%) - 3043 spectra/s] 10.6s
  3. TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 34406/34406 (100%) - 3106 spectra/s] 11.1s
  4. TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 33027/33027 (100%) - 3905 spectra/s] 8.5s
  5. TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.mzBIN_calibrated 1.2 s [progress: 32277/32277 (100%) - 2931 spectra/s] 11.0s
  6. TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 29104/29104 (100%) - 4220 spectra/s] 6.9s
  7. TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.mzBIN_calibrated 0.5 s [progress: 19477/19477 (100%) - 5982 spectra/s] 3.3s
  8. TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 19810/19810 (100%) - 3877 spectra/s] 5.1s
  9. TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.mzBIN_calibrated 1.5 s [progress: 30690/30690 (100%) - 2703 spectra/s] 11.4s
  10. TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.mzBIN_calibrated 1.8 s [progress: 27363/27363 (100%) - 2932 spectra/s] 9.3s
  11. TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.mzBIN_calibrated 2.2 s [progress: 38255/38255 (100%) - 3207 spectra/s] 11.9s
  12. TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.mzBIN_calibrated 1.7 s [progress: 40252/40252 (100%) - 3356 spectra/s] 12.0s
  13. TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.mzBIN_calibrated 1.5 s [progress: 41030/41030 (100%) - 3929 spectra/s] 10.4s
  14. TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 38618/38618 (100%) - 4326 spectra/s] 8.9s
  15. TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.mzBIN_calibrated 1.1 s [progress: 34045/34045 (100%) - 5549 spectra/s] 6.1s
  16. TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 26323/26323 (100%) - 3102 spectra/s] 8.5s
  17. TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.mzBIN_calibrated 1.6 s [progress: 33300/33300 (100%) - 2786 spectra/s] 12.0s
  18. TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.mzBIN_calibrated 1.5 s [progress: 35825/35825 (100%) - 3214 spectra/s] 11.1s
  19. TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.mzBIN_calibrated 1.7 s [progress: 35507/35507 (100%) - 3429 spectra/s] 10.4s
  20. TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.mzBIN_calibrated 2.2 s [progress: 36774/36774 (100%) - 3666 spectra/s] 10.0s
  21. TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.mzBIN_calibrated 1.6 s [progress: 41713/41713 (100%) - 4151 spectra/s] 10.0s
  22. TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.mzBIN_calibrated 1.5 s [progress: 41156/41156 (100%) - 3770 spectra/s] 10.9s
  23. TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzBIN_calibrated 1.9 s [progress: 34620/34620 (100%) - 3132 spectra/s] 11.1s
  24. TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.mzBIN_calibrated 1.7 s [progress: 29308/29308 (100%) - 2767 spectra/s] 10.6s
  25. TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.mzBIN_calibrated 1.6 s [progress: 30239/30239 (100%) - 3703 spectra/s] 8.2s
  26. TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 34665/34665 (100%) - 3886 spectra/s] 8.9s Operating on slice 2 of 5: Fragment index slice generated in 2.97 s
  27. TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.mzBIN_calibrated 0.5 s [progress: 12215/12215 (100%) - 11427 spectra/s] 1.1s
  28. TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 32345/32345 (100%) - 8024 spectra/s] 4.0s
  29. TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.mzBIN_calibrated 1.5 s [progress: 34406/34406 (100%) - 8813 spectra/s] 3.9s
  30. TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.mzBIN_calibrated 1.2 s [progress: 33027/33027 (100%) - 11893 spectra/s] 2.8s
  31. TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 32277/32277 (100%) - 8114 spectra/s] 4.0s
  32. TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.mzBIN_calibrated 1.0 s [progress: 29104/29104 (100%) - 12659 spectra/s] 2.3s
  33. TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.mzBIN_calibrated 0.7 s [progress: 19477/19477 (100%) - 17328 spectra/s] 1.1s
  34. TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.mzBIN_calibrated 0.9 s [progress: 19810/19810 (100%) - 7159 spectra/s] 2.8s
  35. TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 30690/30690 (100%) - 6011 spectra/s] 5.1s
  36. TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.mzBIN_calibrated 1.5 s [progress: 27363/27363 (100%) - 7432 spectra/s] 3.7s
  37. TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.mzBIN_calibrated 1.5 s [progress: 38255/38255 (100%) - 8463 spectra/s] 4.5s
  38. TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.mzBIN_calibrated 1.8 s [progress: 40252/40252 (100%) - 9941 spectra/s] 4.0s
  39. TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 41030/41030 (100%) - 11733 spectra/s] 3.5s
  40. TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 38618/38618 (100%) - 14203 spectra/s] 2.7s
  41. TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.mzBIN_calibrated 1.2 s [progress: 34045/34045 (100%) - 17806 spectra/s] 1.9s
  42. TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 26323/26323 (100%) - 6460 spectra/s] 4.1s
  43. TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.mzBIN_calibrated 1.7 s [progress: 33300/33300 (100%) - 6425 spectra/s] 5.2s
  44. TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.mzBIN_calibrated 1.7 s [progress: 35825/35825 (100%) - 8583 spectra/s] 4.2s
  45. TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 35507/35507 (100%) - 10076 spectra/s] 3.5s
  46. TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.mzBIN_calibrated 1.6 s [progress: 36774/36774 (100%) - 11893 spectra/s] 3.1s
  47. TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.mzBIN_calibrated 1.5 s [progress: 41713/41713 (100%) - 12455 spectra/s] 3.3s
  48. TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.mzBIN_calibrated 1.7 s [progress: 41156/41156 (100%) - 10102 spectra/s] 4.1s
  49. TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzBIN_calibrated 1.6 s [progress: 34620/34620 (100%) - 7460 spectra/s] 4.6s
  50. TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.mzBIN_calibrated 1.6 s [progress: 29308/29308 (100%) - 6570 spectra/s] 4.5s
  51. TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 30239/30239 (100%) - 9287 spectra/s] 3.3s
  52. TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.mzBIN_calibrated 0.3 s [progress: 34665/34665 (100%) - 11475 spectra/s] 3.0s Operating on slice 3 of 5: Fragment index slice generated in 2.96 s
  53. TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 12215/12215 (100%) - 16642 spectra/s] 0.7s
  54. TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 32345/32345 (100%) - 13338 spectra/s] 2.4s
  55. TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.mzBIN_calibrated 1.6 s [progress: 34406/34406 (100%) - 14554 spectra/s] 2.4s
  56. TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 33027/33027 (100%) - 19247 spectra/s] 1.7s
  57. TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 32277/32277 (100%) - 14320 spectra/s] 2.3s
  58. TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.mzBIN_calibrated 1.1 s [progress: 29104/29104 (100%) - 23154 spectra/s] 1.3s
  59. TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.mzBIN_calibrated 0.5 s [progress: 19477/19477 (100%) - 30624 spectra/s] 0.6s
  60. TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 19810/19810 (100%) - 10350 spectra/s] 1.9s
  61. TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 30690/30690 (100%) - 10223 spectra/s] 3.0s
  62. TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 27363/27363 (100%) - 12075 spectra/s] 2.3s
  63. TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 38255/38255 (100%) - 14312 spectra/s] 2.7s
  64. TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.mzBIN_calibrated 1.7 s [progress: 40252/40252 (100%) - 18058 spectra/s] 2.2s
  65. TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.mzBIN_calibrated 2.0 s [progress: 41030/41030 (100%) - 21193 spectra/s] 1.9s
  66. TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.mzBIN_calibrated 1.2 s [progress: 38618/38618 (100%) - 23942 spectra/s] 1.6s
  67. TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.mzBIN_calibrated 1.0 s [progress: 34045/34045 (100%) - 25890 spectra/s] 1.3s
  68. TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 26323/26323 (100%) - 11111 spectra/s] 2.4s
  69. TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.mzBIN_calibrated 1.7 s [progress: 33300/33300 (100%) - 12256 spectra/s] 2.7s
  70. TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.mzBIN_calibrated 1.9 s [progress: 35825/35825 (100%) - 15782 spectra/s] 2.3s
  71. TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.mzBIN_calibrated 2.1 s [progress: 35507/35507 (100%) - 18190 spectra/s] 2.0s
  72. TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.mzBIN_calibrated 1.6 s [progress: 36774/36774 (100%) - 18956 spectra/s] 1.9s
  73. TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.mzBIN_calibrated 1.5 s [progress: 41713/41713 (100%) - 19611 spectra/s] 2.1s
  74. TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.mzBIN_calibrated 1.6 s [progress: 41156/41156 (100%) - 15989 spectra/s] 2.6s
  75. TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzBIN_calibrated 1.6 s [progress: 34620/34620 (100%) - 13848 spectra/s] 2.5s
  76. TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.mzBIN_calibrated 2.5 s [progress: 29308/29308 (100%) - 12974 spectra/s] 2.3s
  77. TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 30239/30239 (100%) - 16488 spectra/s] 1.8s
  78. TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.mzBIN_calibrated 1.5 s [progress: 34665/34665 (100%) - 17998 spectra/s] 1.9s Operating on slice 4 of 5: Fragment index slice generated in 3.22 s
  79. TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 12215/12215 (100%) - 22250 spectra/s] 0.5s
  80. TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 32345/32345 (100%) - 16926 spectra/s] 1.9s
  81. TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.mzBIN_calibrated 2.7 s [progress: 34406/34406 (100%) - 18998 spectra/s] 1.8s
  82. TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.mzBIN_calibrated 1.2 s [progress: 33027/33027 (100%) - 23490 spectra/s] 1.4s
  83. TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 32277/32277 (100%) - 18103 spectra/s] 1.8s
  84. TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.mzBIN_calibrated 1.1 s [progress: 29104/29104 (100%) - 27023 spectra/s] 1.1s
  85. TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.mzBIN_calibrated 0.5 s [progress: 19477/19477 (100%) - 30867 spectra/s] 0.6s
  86. TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.mzBIN_calibrated 0.8 s [progress: 19810/19810 (100%) - 15440 spectra/s] 1.3s
  87. TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 30690/30690 (100%) - 13604 spectra/s] 2.3s
  88. TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.mzBIN_calibrated 0.3 s [progress: 27363/27363 (100%) - 15992 spectra/s] 1.7s
  89. TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 38255/38255 (100%) - 17556 spectra/s] 2.2s
  90. TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 40252/40252 (100%) - 19352 spectra/s] 2.1s
  91. TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 41030/41030 (100%) - 21894 spectra/s] 1.9s
  92. TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 38618/38618 (100%) - 23853 spectra/s] 1.6s
  93. TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.mzBIN_calibrated 0.3 s [progress: 34045/34045 (100%) - 28585 spectra/s] 1.2s
  94. TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.mzBIN_calibrated 0.3 s [progress: 26323/26323 (100%) - 15412 spectra/s] 1.7s
  95. TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 33300/33300 (100%) - 14612 spectra/s] 2.3s
  96. TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 35825/35825 (100%) - 18325 spectra/s] 2.0s
  97. TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 35507/35507 (100%) - 20186 spectra/s] 1.8s
  98. TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 36774/36774 (100%) - 19540 spectra/s] 1.9s
  99. TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 41713/41713 (100%) - 21196 spectra/s] 2.0s
  100. TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.mzBIN_calibrated 0.5 s [progress: 41156/41156 (100%) - 18888 spectra/s] 2.2s
  101. TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 34620/34620 (100%) - 16132 spectra/s] 2.1s
  102. TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 29308/29308 (100%) - 14145 spectra/s] 2.1s
  103. TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 30239/30239 (100%) - 18666 spectra/s] 1.6s
  104. TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.mzBIN_calibrated 0.3 s [progress: 34665/34665 (100%) - 21531 spectra/s] 1.6s Operating on slice 5 of 5: Fragment index slice generated in 3.55 s
  105. TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 12215/12215 (100%) - 22372 spectra/s] 0.5s | remapping alternative proteins and postprocessing 5.3 s
  106. TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 32345/32345 (100%) - 18040 spectra/s] 1.8s | remapping alternative proteins and postprocessing 9.3 s
  107. TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 34406/34406 (100%) - 17545 spectra/s] 2.0s | remapping alternative proteins and postprocessing 9.5 s
  108. TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.mzBIN_calibrated 1.1 s [progress: 33027/33027 (100%) - 23524 spectra/s] 1.4s | remapping alternative proteins and postprocessing 8.4 s
  109. TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.mzBIN_calibrated 1.7 s [progress: 32277/32277 (100%) - 18820 spectra/s] 1.7s | remapping alternative proteins and postprocessing 8.7 s
  110. TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.mzBIN_calibrated 0.9 s [progress: 29104/29104 (100%) - 27225 spectra/s] 1.1s | remapping alternative proteins and postprocessing 7.4 s
  111. TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.mzBIN_calibrated 0.4 s [progress: 19477/19477 (100%) - 31213 spectra/s] 0.6s | remapping alternative proteins and postprocessing 5.1 s
  112. TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.mzBIN_calibrated 1.1 s [progress: 19810/19810 (100%) - 16817 spectra/s] 1.2s | remapping alternative proteins and postprocessing 6.2 s
  113. TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.mzBIN_calibrated 1.6 s [progress: 30690/30690 (100%) - 15037 spectra/s] 2.0s | remapping alternative proteins and postprocessing 8.5 s
  114. TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 27363/27363 (100%) - 17440 spectra/s] 1.6s | remapping alternative proteins and postprocessing 7.5 s
  115. TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.mzBIN_calibrated 1.6 s [progress: 38255/38255 (100%) - 18588 spectra/s] 2.1s | remapping alternative proteins and postprocessing 9.6 s
  116. TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.mzBIN_calibrated 1.6 s [progress: 40252/40252 (100%) - 22141 spectra/s] 1.8s | remapping alternative proteins and postprocessing 9.9 s
  117. TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 41030/41030 (100%) - 24717 spectra/s] 1.7s | remapping alternative proteins and postprocessing 8.0 s
  118. TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.mzBIN_calibrated 1.2 s [progress: 38618/38618 (100%) - 27984 spectra/s] 1.4s | remapping alternative proteins and postprocessing 7.4 s
  119. TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.mzBIN_calibrated 1.2 s [progress: 34045/34045 (100%) - 31937 spectra/s] 1.1s | remapping alternative proteins and postprocessing 5.8 s
  120. TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 26323/26323 (100%) - 14722 spectra/s] 1.8s | remapping alternative proteins and postprocessing 7.2 s
  121. TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.mzBIN_calibrated 1.5 s [progress: 33300/33300 (100%) - 15402 spectra/s] 2.2s | remapping alternative proteins and postprocessing 8.8 s
  122. TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.mzBIN_calibrated 1.7 s [progress: 35825/35825 (100%) - 19577 spectra/s] 1.8s | remapping alternative proteins and postprocessing 8.3 s
  123. TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 35507/35507 (100%) - 21664 spectra/s] 1.6s | remapping alternative proteins and postprocessing 7.6 s
  124. TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.mzBIN_calibrated 1.6 s [progress: 36774/36774 (100%) - 23056 spectra/s] 1.6s | remapping alternative proteins and postprocessing 7.3 s
  125. TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 41713/41713 (100%) - 24479 spectra/s] 1.7s | remapping alternative proteins and postprocessing 7.6 s
  126. TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.mzBIN_calibrated 1.4 s [progress: 41156/41156 (100%) - 21684 spectra/s] 1.9s | remapping alternative proteins and postprocessing 8.0 s
  127. TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 34620/34620 (100%) - 17224 spectra/s] 2.0s | remapping alternative proteins and postprocessing 9.3 s
  128. TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 29308/29308 (100%) - 16273 spectra/s] 1.8s | remapping alternative proteins and postprocessing 7.5 s
  129. TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.mzBIN_calibrated 1.3 s [progress: 30239/30239 (100%) - 20254 spectra/s] 1.5s | remapping alternative proteins and postprocessing 6.3 s
  130. TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.mzBIN_calibrated 1.0 s [progress: 34665/34665 (100%) - 24939 spectra/s] 1.4s | remapping alternative proteins and postprocessing 8.4 s MAIN SEARCH DONE IN 14.781 MIN

***TOTAL TIME 53.162 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F20_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F21_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F22_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F23_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F26_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F28_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F29_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_111028_TY_BN3_AspN_SCX_10percent_F07_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F03_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F04_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F05_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F06_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F08_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F09_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F10_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F11_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F12_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F13_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F14_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F15_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F16_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F17_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.pepXML C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Fragpipe_19.2\lib\fragpipe-19.2-build28.jar;/C:/Fragpipe_19.2/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\X10_Rat_Proteogenomics_01\02_mzML_files\04_BN_AspN_TTOF_WIFF\TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.pin C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F18_recal_371_445-BN3_AspN.pin Process 'MSFragger move pin' finished, exit code: 0

Please cite: (Any searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14:513 (2017) (Any searches) Fast deisotoping algorithm and its implementation in the MSFragger search engine. J. Proteome Res. 20:498 (2021) (Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020) (Glyco/labile search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 17:1125 (2020) (timsTOF PASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19:1575 (2020) (Visualization with FragPipe-PDV) PDV: an integrative proteomics data viewer. Bioinformatics. 35(7):1249 (2019)

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danielgeiszler commented 1 year ago

Thank you. Can you also please upload the full log from the combined run that failed?

TeckYewLow commented 1 year ago

Sure Daniel,

This is the full log for the 1st combined run which stalled at MSBooster: https://drive.google.com/file/d/1s1dw2cz_uPpJXTWn64IoyqNdAPSpyjq-/view?usp=sharing

This is the full log for the 2nd combined run which stalled at Percolator: https://drive.google.com/file/d/1s3Hz7cgydyH_RwSEBSdqt5hgSWa-Lz1J/view?usp=sharing

Thanks! 👍

fcyu commented 1 year ago

@TeckYewLow Could you share TT1_110911_TY_BN3_AspN_SCX_10percent_F27_recal_371_445-BN3_AspN.pin with us? Please ZIP the file and drag the file to the issue dialog.

Best,

Fengchao

TeckYewLow commented 1 year ago

Sure @fcyu Downloads.zip

fcyu commented 1 year ago

I guess it was due to some file system issue that FragPipe could not read the file properly. Could you rerun and try again?

Thanks,

Fengchao

TeckYewLow commented 1 year ago

Hi @fcyu

I have two samples i.e. BN and SHR, and each was digested with 5 different proteases. So all together I have 10 datasets. First I tried to analyzed all 10 datasets in one go, and it gave me error message.

Then I tried to run BN only (5 datasets) and it worked. I also tried to analyze another 5 datasets from SHR, and it worked too. It did not work only when I analyzed all 10 datasets.

Best,

Teck

fcyu commented 1 year ago

Could you share the log files? Please zip and upload here.

Best,

Fengchao

TeckYewLow commented 1 year ago

@fcyu

Here is the zipped files. Thank you so much!

Best,

Teck 20230403_RAT_COMBINED.zip

fcyu commented 1 year ago

The error was from MSBooster:

Processing TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN.mzML
RT regression using 1744 PSMs
Edited pin file at C:\Fragpipe_19.2\Results\RAT_COMBINED\BnAspnTT\TT1_110911_TY_BN3_AspN_SCX_10percent_F24_recal_371_445-BN3_AspN_edited.pin
Processing TT1_110911_TY_BN3_AspN_SCX_10percent_F25_recal_371_445-BN3_AspN.mzML
umich.ms.fileio.exceptions.FileParsingException: java.util.concurrent.TimeoutException
    at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:198)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:807)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:791)
    at Features.mzMLReader.<init>(mzMLReader.java:72)
    at Features.percolatorFormatter.editPin(percolatorFormatter.java:322)
    at Features.MainClass.main(MainClass.java:588)
Caused by: java.util.concurrent.TimeoutException
    at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:204)
    at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:191)
    ... 5 more
Process 'MSBooster' finished, exit code: 1
Process returned non-zero exit code, stopping

Need Kevin @yangkl96 to take a look.

Best,

Fengchao Need Kevin to take a look.

Best,

Fengchao

yangkl96 commented 1 year ago

Hi @TeckYewLow ,

Looking at the different log files, MSBooster failed when processing different files, but with the same timeout error. I noticed FragPipe was only using 5 or 6 GB of RAM. Could you retry this and set "RAM" and "Parallelism" in the Workflow tab to 0, and close all other programs like Google Chrome?

On a separate note, the unweighted spectral entropy score in your pin file had all rows with value 0, indicating that MSBooster may have issues extracting m/z values from the mzml files. Did you convert wiff files to mzml files? If so, could you share the details of how you converted them? Or you can share a single mzml file here so I can test?

Thanks, Kevin

rugenni commented 1 year ago

Hi everyone,

I am also trying to analyze a multi-protease dataset with fragpipe 20 and tried the workaround suggested by Fengchao.

Did this actually work for anyone? I also get error messages from MSBooster that it cannot find some files (log file attached).

Since I am coming from the MaxQuant world I assume that some of my settings are wrong. Your help would be highly appreciated!

Cheers, Nils

log_2023-06-20_16-58-07.txt

fcyu commented 1 year ago

Hi Nils,

Your error was due to a missing file E:\MS-Fragger_Multi-Protease_timsFractionation\fragger.params.

The approach I suggested is kind of "advanced". It requires you to re-organize the files carefully to "fool" FragPipe.

Best,

Fengchao

rugenni commented 1 year ago

Hi Fengchao,

thanks for the quick reply. I would like to give it a try since data look way better than with MaxQuant :)

So I played with two different digests for now. Each digest has its own fragger.params file, right? After moving one of them in the folder (does this matter?), MSBooster now misses [SAMPLE-NAME]_uncalibrated.pin.

Fragger only generated [SAMPLE-NAME].pin.

Thanks, Nils

fcyu commented 1 year ago

Hi Nils,

Your input mzML file names have suffix _uncalibrated. That is why MSBooster looked for the [SAMPLE-NAME]_uncalibrated.pin.

Could you specify the original files (the ones without _uncalibrated suffix) in FragPipe?

Best,

Fengchao

rugenni commented 1 year ago

Hi Fengchao,

thanks again for the quick help, highly appreciated.

Now it worked without any error.

Best, Nils

anesvi commented 1 year ago

Hi Nils If you are able to run it, can you send me a short tutorial so we can post on our website. I think others will benefit from it. If you can email me at nesvi at med.umich.edu I would appreciate it Thanks, Alexey

rugenni commented 1 year ago

Hi Alexey,

sure, I can do that.

I will try the workflow with more samples and proteases to double check first.

Best, Nils