With .d as input, the latest msconverter does not write `mean inverse reduced ion mobility array` array to the mzML file.

[jd690764]

Describe the bug A clear and concise description of what the bug is.

I have a similar problem to #579, but the error happens in IonQuant (please see the attached log file).

I am working with timstof data from a phospho workflow that I used successfully in the past. The .d files were converted with msconvert using the params shown in the second attachment.

Could you please look into this - any help is greatly appreciated.

Thanks Janos

---

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[fcyu]

Hi @jd690764 ,

This is weird. You are the second one having the same issue. Can you help me with the following two things:

1. Are your mzML file has ion mobility array? You can open one mzml file using a text editor (I recommend glogg, VS code, and sublime text), and search for name="mean inverse reduced ion mobility array" in the mzML file. Following is the example with ion mobility, mz, and intensity arrays:

2. If your mzML file does not have any ion mobility array, can you tell me the version of your msconverter? If possible, can you send me one of your mzML files?

Thanks,

Fengchao

[jd690764]

Hi Fengchao,

Thank you for getting back to me.

I don't see that field in the mzML file. I also checked an earlier set of samples that finished ionquant analysis, but I did not see this text in that one either. On the other hand, both of them have "inverse reduced ion mobility". The context - in both of them - looks like this:

    <spectrum index="3" id="merged=6 frame=7 scanStart=551 scanEnd=575"

defaultArrayLength="106"> <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/> <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/> <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/> <cvParam cvRef="MS" accession="MS:1000796" name="spectrum title" value="210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.4.4.2 File:"210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.d", NativeID:"merged=6 frame=7 scanStart=551 scanEnd=575", IonMobility:"1.0322508569619999""/> <userParam name="ion mobility lower limit" value="1.0262688153061592" type="xsd:double" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/> <userParam name="ion mobility upper limit" value="1.0385112828640728" type="xsd:double" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>

I am using MSconvert Version: 3.0.21323-cf4035a. I must have used this same version with the earlier, successful, run because the preset is present only in the current version.

If you still need it, can you send me a link to a folder to upload the mzML file?

Thanks, Janos

On Fri, Jan 14, 2022 at 12:40 PM Fengchao @.***> wrote:

Hi @jd690764 https://github.com/jd690764 ,

This is weird. You are the second one having the same issue. Can you help me with the following two things:

1.

Are your mzML file has ion mobility array? You can open one mzml file using a text editor (I recommend glogg, VS code, and sublime text), and search for name="mean inverse reduced ion mobility array" in the mzML file. Following is the example with ion mobility, mz, and intensity arrays: [image: image] https://user-images.githubusercontent.com/6926299/149582063-afa981d8-310b-4aca-a39a-f6b27b7cfa75.png 2.

If your mzML file does not have any ion mobility array, can you tell me the version of your msconverter? If possible, can you send me one of your mzML files?

Thanks,

Fengchao

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[fcyu]

Hi Janos,

Here is the link: https://www.dropbox.com/request/mJ9FdmApG33lU7ysWMep

Thanks,

Fengchao

[jd690764]

Hi Fengchao,

I uploaded one - let me know if I can help with something else.

Thanks, Janos

On Fri, Jan 14, 2022 at 5:23 PM Fengchao @.***> wrote:

Hi Janos,

Here is the link: https://www.dropbox.com/request/mJ9FdmApG33lU7ysWMep

Thanks,

Fengchao

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[fcyu]

Hi Janos,

Thanks for your file. I have confirmed that you file also don't have the ion mobility array:

I converted one of my .d files using the latest msconverter, and there is also no ion mobility array, which is different from what I have from an older version of msconverter.

I need to contact msconverter's developer regarding the missing of ion mobility array.

Best,

Fengchao

[fcyu]

Hi Janos,

The ProteoWizard developer answered my questions (https://github.com/ProteoWizard/pwiz/issues/1946). Basically, enabling scanSumming will discard ion mobility array, which makes the file unsuitable for MS1-based quantification. I will update the tutorial by adding that note.

Best,

Fengchao

[KR-15]

Hi all,

I have converted again the .d into mzML without the scansumming and it works well for me, I succeed to finish the LFQ-phospho worfklow without any error message. Just as a remainder, mzML files were necessary here in order to allow the PTMProphet option for phospho localization score.

Best,

KR

[fcyu]

Hi KR,

Thanks for your feedback. I am just wondering what the result looks like without scanSumming. We never thoroughly tested the identification sensitivity without scanSumming.

Best,

Fengchao

[jd690764]

Hi Fengchao,

I am a bit confused now. I ran this workflow in the past using mzML files converted with MSconvert Version: 3.0.21323 with ScanSumming among the filters, and containing no "mean inverse reduced ion mobility array". These runs finished without producing errors by IonQuant.

This suggests the error is not caused by the lack of the tag. Also, do you think these earlier analyses should be repeated without the filter?

Thank you for your help. Janos

On Tue, Jan 18, 2022 at 7:16 AM Fengchao @.***> wrote:

Hi KR,

Thanks for your feedback. I am just wondering what the result looks like without scanSumming. We never thoroughly tested the identification sensitivity without scanSumming.

Best,

Fengchao

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[fcyu]

I am a bit confused now. I ran this workflow in the past using mzML files converted with MSconvert Version: 3.0.21323 with ScanSumming among the filters, and containing no "mean inverse reduced ion mobility array". These runs finished without producing errors by IonQuant.

I don't think IonQuant would finish without error if you specified IM-MS (ion mobility, timsTOF only) here:

If you specified Regular MS, there wouldn't be any error because IonQuant treat your mzML file as regular MS without ion mobility. But, it is not optimal for ddaPASEF data.

Best,

Fengchao

[KR-15]

Hi Janos, Fengchao,

I would like to know if, in the future, it would be possible to do the LFQ-phospho workflow with PTMProphet activated without the conversion to mzML with ddaPASEF files (.d) in order to be sure that MSConvert does not modify anything during the conversion ? Because, working with .d files seems to work with this LFQ-phospho worfklow when we uncheck the PTM-Prophet in the Validation tab of FragPipe.

Is it possible to have your older version of MSConvert which allows us to use the scansumming option ? I did not found it in ProteoWizard website. Because I wanted to run and compare the analysis with the mzML conversion using your older version of MSConvert (with the scansumming option and the presence of name="mean inverse reduced ion mobility array") compared with the one with the recent version of MS convert that I use (version 3.0.21266) (without the scansumming filter in order to get the ion mobility array). In that way, I could compare both analysis to see if there is drastic changes.

Thanks for your help.

Best,

KR

[fcyu]

Hi KR,

I would like to know if, in the future, it would be possible to do the LFQ-phospho workflow with PTMProphet activated without the conversion to mzML with ddaPASEF files (.d) in order to be sure that MSConvert does not modify anything during the conversion ? Because, working with .d files seems to work with this LFQ-phospho worfklow when we uncheck the PTM-Prophet in the Validation tab of FragPipe.

We generate *_uncalibrated.mgf for each .d, if PTMProphet can read that file, then we don't need to convert .d. But, since PTMProphet is maintained by the TPP guys, I am not sure if it is easy to change PTMProphet.

Is it possible to have your older version of MSConvert which allows us to use the scansumming option ? I did not found it in ProteoWizard website. Because I wanted to run and compare the analysis with the mzML conversion using your older version of MSConvert (with the scansumming option and the presence of name="mean inverse reduced ion mobility array") compared with the one with the recent version of MS convert that I use (version 3.0.21266) (without the scansumming filter in order to get the ion mobility array). In that way, I could compare both analysis to see if there is drastic changes.

The scanSumming is available in all versions. You can use the latest version to do the comparison.

Best,

Fengchao

[KR-15]

Hi Fengchao,

The scanSumming is available in all versions. You can use the latest version to do the comparison.

Yes but if I am using the scanSumming option in the recent version that I used I will loss the ion mobility array and therefore cannot make the comparison because the mzML files of this workflow won't have a ion mobility array. I need the ion mobility array to compare the following:

• LFQ-phospho workflow with mzML made without the scan summing option (in order to have the ion mobility array with recent version of MSconvert)
• LFQ-phospho workflow with mzML made with the scan summing option (in order to have the ion mobility array with your older version of MSconvert because you previously said that it was working well with older version of MSConvert)

With the old msconverter (e.g. 3.0.21016), there are mean inverse reduced ion mobility array in the mzML converted from .d ddaPASEF. However, with the latest version, that array is gone, which crashes the MS1 quantification in IonQuant (Nesvilab/FragPipe#581).

The goal is too check if there is a difference using or not this scansumming filter on the results because you said:

I am just wondering what the result looks like without scanSumming. We never thoroughly tested the identification sensitivity without scanSumming.

Best,

KR

[fcyu]

Hi KR,

LFQ-phospho workflow with mzML made without the scan summing option (in order to have the ion mobility array with recent version of MSconvert)

Yes, you can.

LFQ-phospho workflow with mzML made with the scan summing option (in order to have the ion mobility array with your older version of MSconvert because you previously said that it was working well with older version of MSConvert)

No, you can't. I said it wrong. Please check my comment here https://github.com/Nesvilab/FragPipe/issues/581#issuecomment-1013909453.

Best,

Fengchao

[KR-15]

Hi Fengchao,

With the old msconverter (e.g. 3.0.21016), there are mean inverse reduced ion mobility array in the mzML converted from .d ddaPASEF. However, with the latest version, that array is gone, which crashes the MS1 quantification in IonQuant (Nesvilab/FragPipe#581).

So you are telling me that the quote above was not correct ? I just want to test if the scanSumming filter has an impact on the final results and the only experiment that I could do is the one explained in my previous post:

LFQ-phospho workflow with mzML made without the scan summing option (in order to have the ion mobility array with recent version of MSconvert) LFQ-phospho workflow with mzML made with the scan summing option (in order to have the ion mobility array with your older version of MSconvert because you previously said that it was working well with older version of MSConvert).

And for doing this, if I understood well, we need the MSConvert version that you used at that time. Because if the scanSumming filter is really important and if we want to made MS1 based quantification with ion mobility, we cannot do it for the moment, therefore the LFQ-phospho with PTMProphet is not usable right with ddaPASEF data?

Do you know if running the mzML conversion without the scanSumming filter in order to have the ion mobility array will have a impact on the final results ?

I think you ask to the MSConvert developpers to correct this bug is that correct ?

Best,

KR

[fcyu]

Hi KR,

So you are telling me that the quote above was not correct ?

You are right, the quote is wrong. Both old and new msconverter don't have ion mobility array with scanSumming. I apologize that I said it incorrectly.

And for doing this, if I understood well, we need the MSConvert version that you used at that time. Because if the scanSumming filter is really important and if we want to made MS1 based quantification with ion mobility, we cannot do it for the moment, therefore the LFQ-phospho with PTMProphet is not usable right with ddaPASEF data?

I think needing to figure out if scanSumming is that important. If you really want to use PTMProphet for ddaPASEF, can turn off scanSumming.

Do you know if running the mzML conversion without the scanSumming filter in order to have the ion mobility array will have a impact on the final results ?

It is supposed to have a difference. I don't know how big it is. Never compared the results with and without scanSumming.

I think you ask to the MSConvert developpers to correct this bug is that correct ?

It is not a bug from my understanding. Here (https://github.com/ProteoWizard/pwiz/issues/1946#issuecomment-1013798506) is the reply from the msconverter developer.

Best,

Fengchao

[jd690764]

Hi Fengchao,

I think the corresponding parameter in the log file should be this one:

msfragger.data_type=0

In previous error-free runs the value was 0, just like in the current run where the gui shows I selected the ion mobility option.

If this is the correct parameter, the reason should be something different, right?

Thanks, Janos

On Tue, Jan 18, 2022 at 6:13 PM Fengchao @.***> wrote:

I am a bit confused now. I ran this workflow in the past using mzML files converted with MSconvert Version: 3.0.21323 with ScanSumming among the filters, and containing no "mean inverse reduced ion mobility array". These runs finished without producing errors by IonQuant.

I don't think IonQuant would finish without error if you specified IM-MS (ion mobility, timsTOF only) here:

[image: image] https://user-images.githubusercontent.com/6926299/150050611-d7f32781-c8bb-49fa-8fe6-f31256b78e7d.png

If you specified Regular MS, there wouldn't be any error because IonQuant treat your mzML file as regular MS without ion mobility. But, it is not optimal for ddaPASEF data.

Best,

Fengchao

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[fcyu]

msfragger.data_type is irrelevant. It tells MSFragger is your data is from DDA, DIA, GPF-DIA, or DIA-Quant.

For your case, it should always be 0.

Best,

Fengchao

[jd690764]

So which parameter should I look at to check what the selection was (with or without ion mobility)?

Thanks, Janos

On Thu, Jan 20, 2022 at 12:36 PM Fengchao @.***> wrote:

msfragger.data_type is irrelevant. It tells MSFragger is your data is from DDA, DIA, GPF-DIA, or DIA-Quant.

For your case, it should always be 0.

Best,

Fengchao

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[fcyu]

workflow.input.data-type.im-ms

Best,

Fengchao

[jd690764]

Thanks, Fengchao!

workflow.input.data-type.im-ms=true

workflow.input.data-type.regular-ms=false

This is what I had in previous error-free runs. Any other potential reasons why IonQuant did not fail?

I attached the log file for one of these previous error-free runs.

Thank you, Janos

On Thu, Jan 20, 2022 at 12:45 PM Fengchao @.***> wrote:

workflow.input.data-type.im-ms

Best,

Fengchao

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System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_311, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 17.1 MSFragger version 3.4 Philosopher version 4.1.1 (build 1637179075)

LCMS files: Experiment/Group: CEP164_NTA_1

• g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.mzML DDA Experiment/Group: CEP164_NTA_2
• g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_Cep164KO_II_Slot2-20_1_9317.mzML DDA Experiment/Group: CEP164_NTA_3
• g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_III_Slot2-12_1_9339.mzML DDA Experiment/Group: CEP164_TiO2_1
• g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_I_Slot2-13_1_9287.mzML DDA Experiment/Group: CEP164_TiO2_2
• g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_II_Slot2-29_1_9320.mzML DDA Experiment/Group: CEP164_TiO2_3
• g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_III_Slot2-13_1_9343.mzML DDA Experiment/Group: TTBK2_K50A_NTA_1
• g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-23_1_9305.mzML DDA Experiment/Group: TTBK2_K50A_TiO2_1
• g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-32_1_9308.mzML DDA Experiment/Group: TTBK2_NTA_1
• g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_I_Slot2-14_1_9291.mzML DDA Experiment/Group: TTBK2_NTA_2
• g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_II_Slot2-21_1_9325.mzML DDA Experiment/Group: TTBK2_NTA_3
• g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.mzML DDA Experiment/Group: TTBK2_TiO2_1
• g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_I_Slot2-15_1_9295.mzML DDA Experiment/Group: TTBK2_TiO2_2
• g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_II_Slot2-30_1_9328.mzML DDA Experiment/Group: TTBK2_TiO2_3
• g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_III_Slot2-15_1_9351.mzML DDA Experiment/Group: TTBK2_wt_NTA_1
• g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-22_1_9299.mzML DDA Experiment/Group: TTBK2_wt_TiO2_1
• g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-31_1_9302.mzML DDA Experiment/Group: wt_NTA_1
• g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_I_Slot2-10_1_9275.mzML DDA Experiment/Group: wt_NTA_2
• g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_II_Slot2-19_1_9311.mzML DDA Experiment/Group: wt_NTA_3
• g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_III_Slot2-10_1_9331.mzML DDA Experiment/Group: wt_TiO2_1
• g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_I_Slot2-11_1_9279.mzML DDA Experiment/Group: wt_TiO2_2
• g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_II_Slot2-28_1_9314.mzML DDA Experiment/Group: wt_TiO2_3
• g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_III_Slot2-11_1_9335.mzML DDA

296 commands to execute: CheckCentroid java -Xmx106G -cp "C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;C:\msfragger2\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" com.dmtavt.fragpipe.util.CheckCentroid g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.mzML 48 WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_3] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_3] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_2] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_2] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_NTA_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_NTA_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_2] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_2] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_2] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_2] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_3] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_3] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_3] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_3] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_TiO2_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_TiO2_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_2] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_2] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_TiO2_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_TiO2_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_2] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_2] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_3] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_3] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_3] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_3] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_3] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_3] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_NTA_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_NTA_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_2] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_2] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_1] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2] java -jar -Dfile.encoding=UTF-8 -Xmx106G C:\msfragger2\FragPipe-17.0\fragpipe\tools\MSFragger-3.4\MSFragger-3.4.jar G:\Mohammad2103\210908\msf_ttbk2_rs2\fragger.params g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.mzML g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_Cep164KO_II_Slot2-20_1_9317.mzML g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_III_Slot2-12_1_9339.mzML g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_I_Slot2-13_1_9287.mzML g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_II_Slot2-29_1_9320.mzML g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_III_Slot2-13_1_9343.mzML g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-23_1_9305.mzML g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-32_1_9308.mzML g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_I_Slot2-14_1_9291.mzML g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_II_Slot2-21_1_9325.mzML g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.mzML g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_I_Slot2-15_1_9295.mzML g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_II_Slot2-30_1_9328.mzML g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_III_Slot2-15_1_9351.mzML g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-22_1_9299.mzML g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-31_1_9302.mzML g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_I_Slot2-10_1_9275.mzML g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_II_Slot2-19_1_9311.mzML g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_III_Slot2-10_1_9331.mzML g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_I_Slot2-11_1_9279.mzML g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_II_Slot2-28_1_9314.mzML g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_III_Slot2-11_1_9335.mzML MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_1\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_1\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_Cep164KO_II_Slot2-20_1_9317.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_2\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_Cep164KO_II_Slot2-20_1_9317.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_Cep164KO_II_Slot2-20_1_9317.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_2\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_Cep164KO_II_Slot2-20_1_9317.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_III_Slot2-12_1_9339.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_3\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_III_Slot2-12_1_9339.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_III_Slot2-12_1_9339.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_3\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_III_Slot2-12_1_9339.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_I_Slot2-13_1_9287.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_1\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_I_Slot2-13_1_9287.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_I_Slot2-13_1_9287.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_1\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_I_Slot2-13_1_9287.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_II_Slot2-29_1_9320.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_2\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_II_Slot2-29_1_9320.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_II_Slot2-29_1_9320.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_2\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_II_Slot2-29_1_9320.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_III_Slot2-13_1_9343.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_3\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_III_Slot2-13_1_9343.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_III_Slot2-13_1_9343.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_3\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_III_Slot2-13_1_9343.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-23_1_9305.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_NTA_1\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-23_1_9305.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-23_1_9305.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_NTA_1\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-23_1_9305.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-32_1_9308.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_TiO2_1\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-32_1_9308.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-32_1_9308.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_TiO2_1\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-32_1_9308.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_I_Slot2-14_1_9291.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_1\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_I_Slot2-14_1_9291.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_I_Slot2-14_1_9291.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_1\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_I_Slot2-14_1_9291.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_II_Slot2-21_1_9325.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_2\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_II_Slot2-21_1_9325.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_II_Slot2-21_1_9325.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_2\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_II_Slot2-21_1_9325.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_3\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_3\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_I_Slot2-15_1_9295.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_1\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_I_Slot2-15_1_9295.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_I_Slot2-15_1_9295.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_1\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_I_Slot2-15_1_9295.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_II_Slot2-30_1_9328.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_2\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_II_Slot2-30_1_9328.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_II_Slot2-30_1_9328.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_2\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_II_Slot2-30_1_9328.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_III_Slot2-15_1_9351.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_3\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_III_Slot2-15_1_9351.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_III_Slot2-15_1_9351.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_3\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_III_Slot2-15_1_9351.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-22_1_9299.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_NTA_1\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-22_1_9299.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-22_1_9299.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_NTA_1\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-22_1_9299.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-31_1_9302.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_TiO2_1\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-31_1_9302.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-31_1_9302.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_TiO2_1\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-31_1_9302.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_I_Slot2-10_1_9275.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_1\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_I_Slot2-10_1_9275.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_I_Slot2-10_1_9275.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_1\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_I_Slot2-10_1_9275.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_II_Slot2-19_1_9311.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_2\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_II_Slot2-19_1_9311.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_II_Slot2-19_1_9311.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_2\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_II_Slot2-19_1_9311.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_III_Slot2-10_1_9331.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_3\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_III_Slot2-10_1_9331.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_III_Slot2-10_1_9331.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_3\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_III_Slot2-10_1_9331.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_I_Slot2-11_1_9279.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_1\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_I_Slot2-11_1_9279.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_I_Slot2-11_1_9279.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_1\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_I_Slot2-11_1_9279.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_II_Slot2-28_1_9314.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_2\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_II_Slot2-28_1_9314.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_II_Slot2-28_1_9314.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_2\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_II_Slot2-28_1_9314.tsv MSFragger move pepxml java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_III_Slot2-11_1_9335.pepXML G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_3\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_III_Slot2-11_1_9335.pepXML MSFragger move tsv java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/msfragger2/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_III_Slot2-11_1_9335.tsv G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_3\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_III_Slot2-11_1_9335.tsv PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_1\fragpipe-210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_2\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_Cep164KO_II_Slot2-20_1_9317.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_3\fragpipe-210910_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_III_Slot2-12_1_9339.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_1\fragpipe-210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_I_Slot2-13_1_9287.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_2\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_II_Slot2-29_1_9320.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_3\fragpipe-210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_III_Slot2-13_1_9343.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_NTA_1\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-23_1_9305.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_TiO2_1\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-32_1_9308.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_1\fragpipe-210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_I_Slot2-14_1_9291.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_2\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_II_Slot2-21_1_9325.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_3\fragpipe-210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_1\fragpipe-210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_I_Slot2-15_1_9295.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_2\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_II_Slot2-30_1_9328.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_3\fragpipe-210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_III_Slot2-15_1_9351.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_NTA_1\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-22_1_9299.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_TiO2_1\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-31_1_9302.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_1\fragpipe-210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_I_Slot2-10_1_9275.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_2\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_II_Slot2-19_1_9311.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_3\fragpipe-210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_III_Slot2-10_1_9331.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_1\fragpipe-210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_I_Slot2-11_1_9279.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_2\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_II_Slot2-28_1_9314.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_3\fragpipe-210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_III_Slot2-11_1_9335.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_1\fragpipe-210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_19283.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_2\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_Cep164KO_II_Slot2-20_19317.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_Cep164KO_II_Slot2-20_1_9317.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_3\fragpipe-210910_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_III_Slot2-12_19339.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_III_Slot2-12_1_9339.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_1\fragpipe-210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_I_Slot2-13_19287.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_I_Slot2-13_1_9287.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_2\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_II_Slot2-29_19320.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_II_Slot2-29_1_9320.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_3\fragpipe-210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_III_Slot2-13_19343.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_III_Slot2-13_1_9343.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_NTA_1\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-23_19305.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-23_1_9305.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_TiO2_1\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-32_19308.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-32_1_9308.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_1\fragpipe-210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_I_Slot2-14_19291.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_I_Slot2-14_1_9291.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_2\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_II_Slot2-21_19325.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_II_Slot2-21_1_9325.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_3\fragpipe-210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_19347.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_1\fragpipe-210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_I_Slot2-15_19295.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_I_Slot2-15_1_9295.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_2\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_II_Slot2-30_19328.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_II_Slot2-30_1_9328.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_3\fragpipe-210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_III_Slot2-15_19351.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_III_Slot2-15_1_9351.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_NTA_1\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-22_19299.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-22_1_9299.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_TiO2_1\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-31_19302.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-31_1_9302.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_1\fragpipe-210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_I_Slot2-10_19275.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_I_Slot2-10_1_9275.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_2\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_II_Slot2-19_19311.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_II_Slot2-19_1_9311.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_3\fragpipe-210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_III_Slot2-10_19331.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_III_Slot2-10_1_9331.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_1\fragpipe-210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_I_Slot2-11_19279.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_I_Slot2-11_1_9279.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_2\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_II_Slot2-28_19314.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_II_Slot2-28_1_9314.pepXML PeptideProphet [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_3\fragpipe-210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_III_Slot2-11_19335.pepXML-temp] C:\msfragger2\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database D:\msf_stuff\protlib\2021-07-27-decoys-contam-human_210720_nodup_nps_msf.fa ..\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_III_Slot2-11_1_9335.pepXML PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_1\fragpipe-210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_2\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_Cep164KO_II_Slot2-20_1_9317.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_3\fragpipe-210910_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_III_Slot2-12_1_9339.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_1\fragpipe-210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_I_Slot2-13_1_9287.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_2\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_II_Slot2-29_1_9320.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_3\fragpipe-210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_III_Slot2-13_1_9343.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_NTA_1\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-23_1_9305.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_TiO2_1\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-32_1_9308.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_1\fragpipe-210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_I_Slot2-14_1_9291.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_2\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_II_Slot2-21_1_9325.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_3\fragpipe-210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_1\fragpipe-210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_I_Slot2-15_1_9295.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_2\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_II_Slot2-30_1_9328.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_3\fragpipe-210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_III_Slot2-15_1_9351.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_NTA_1\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-22_1_9299.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_TiO2_1\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-31_1_9302.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_1\fragpipe-210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_I_Slot2-10_1_9275.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_2\fragpipe-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_II_Slot2-19_1_9311.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_3\fragpipe-210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_III_Slot2-10_1_9331.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_1\fragpipe-210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_I_Slot2-11_1_9279.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_2\fragpipe-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_II_Slot2-28_1_9314.pepXML-temp PeptideProphet: Delete temp java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_3\fragpipe-210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_III_Slot2-11_1_9335.pepXML-temp Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_3] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_3\interact-210910_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_III_Slot2-12_1_9339.pep.xml g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_III_Slot2-12_1_9339.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_1] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_1\interact-210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_I_Slot2-14_1_9291.pep.xml g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_I_Slot2-14_1_9291.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_NTA_1] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_NTA_1\interact-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-23_1_9305.pep.xml g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-23_1_9305.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_2] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_2\interact-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_II_Slot2-19_1_9311.pep.xml g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_II_Slot2-19_1_9311.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_2] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_2\interact-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_Cep164KO_II_Slot2-20_1_9317.pep.xml g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_Cep164KO_II_Slot2-20_1_9317.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_2] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_2\interact-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_II_Slot2-28_1_9314.pep.xml g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_II_Slot2-28_1_9314.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_2] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_2\interact-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_II_Slot2-21_1_9325.pep.xml g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_II_Slot2-21_1_9325.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_NTA_1] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_NTA_1\interact-210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-22_1_9299.pep.xml g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-22_1_9299.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_3] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_3\interact-210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_III_Slot2-11_1_9335.pep.xml g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_III_Slot2-11_1_9335.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_1] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_1\interact-210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_I_Slot2-10_1_9275.pep.xml g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_I_Slot2-10_1_9275.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_1] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_NTA_1\interact-210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.pep.xml g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_2] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_2\interact-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_II_Slot2-29_1_9320.pep.xml g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_II_Slot2-29_1_9320.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_3] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_3\interact-210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_III_Slot2-13_1_9343.pep.xml g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_III_Slot2-13_1_9343.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_2] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_2\interact-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_II_Slot2-30_1_9328.pep.xml g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_II_Slot2-30_1_9328.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_1] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_TiO2_1\interact-210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_I_Slot2-11_1_9279.pep.xml g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_I_Slot2-11_1_9279.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_3] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_NTA_3\interact-210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.pep.xml g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_3] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_3\interact-210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_III_Slot2-15_1_9351.pep.xml g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_III_Slot2-15_1_9351.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_1] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_TiO2_1\interact-210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_I_Slot2-15_1_9295.pep.xml g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_I_Slot2-15_1_9295.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_1] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\CEP164_TiO2_1\interact-210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_I_Slot2-13_1_9287.pep.xml g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_I_Slot2-13_1_9287.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_3] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\wt_NTA_3\interact-210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_III_Slot2-10_1_9331.pep.xml g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_III_Slot2-10_1_9331.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_TiO2_1] java -cp C:\msfragger2\FragPipe-17.1\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_wt_TiO2_1\interact-210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-31_1_9302.pep.xml g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-31_1_9302.mzML Rewrite pepxml [Work dir: G:\Mohammad2103\210908\msf_ttbk2_rs2\TTBK2_K50A_TiO2_1]

[fcyu]

The log was truncated by GitHub, please send it to yufe@umich.edu. If you believe that your mzML is with scanSumming and have ion mobility array, can you send one of your mzML files to me?

Thanks,

Fengchao

[jd690764]

The mzML was done with scanSumming but did not have ion mobility array.

Janos

On Thu, Jan 20, 2022 at 1:00 PM Fengchao @.***> wrote:

The log was truncated by GitHub, please send it to @.*** If you believe that your mzML is with scanSumming and have ion mobility array, can you send one of your mzML files to me?

Thanks,

Fengchao

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/581#issuecomment-1017922684, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACP7QYY26AMK5NW4MJYK36LUXBZVFANCNFSM5L7VGG4A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

[fcyu]

Hmm, IonQuant detected that there were .d folders and was using them for quantification. This is actually a feasible workaround.

2022-01-04 00:58:26 [INFO] - Checking g:\Mohammad_2103_\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.d...
2022-01-04 00:58:28 [INFO] - Checking g:\Mohammad_2103_\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_Cep164KO_II_Slot2-20_1_9317.d...
2022-01-04 00:58:29 [INFO] - Checking g:\Mohammad_2103_\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_III_Slot2-12_1_9339.d...
2022-01-04 00:58:31 [INFO] - Checking g:\Mohammad_2103_\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_I_Slot2-13_1_9287.d...
2022-01-04 00:58:32 [INFO] - Checking g:\Mohammad_2103_\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_II_Slot2-29_1_9320.d...
2022-01-04 00:58:34 [INFO] - Checking g:\Mohammad_2103_\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_III_Slot2-13_1_9343.d...
2022-01-04 00:58:35 [INFO] - Checking g:\Mohammad_2103_\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-23_1_9305.d...
2022-01-04 00:58:36 [INFO] - Checking g:\Mohammad_2103_\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-32_1_9308.d...
2022-01-04 00:58:37 [INFO] - Checking g:\Mohammad_2103_\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_I_Slot2-14_1_9291.d...
2022-01-04 00:58:38 [INFO] - Checking g:\Mohammad_2103_\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_II_Slot2-21_1_9325.d...
2022-01-04 00:58:40 [INFO] - Checking g:\Mohammad_2103_\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.d...
2022-01-04 00:58:41 [INFO] - Checking g:\Mohammad_2103_\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_I_Slot2-15_1_9295.d...
2022-01-04 00:58:42 [INFO] - Checking g:\Mohammad_2103_\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_II_Slot2-30_1_9328.d...
2022-01-04 00:58:43 [INFO] - Checking g:\Mohammad_2103_\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_III_Slot2-15_1_9351.d...
2022-01-04 00:58:44 [INFO] - Checking g:\Mohammad_2103_\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-22_1_9299.d...
2022-01-04 00:58:45 [INFO] - Checking g:\Mohammad_2103_\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-31_1_9302.d...
2022-01-04 00:58:46 [INFO] - Checking g:\Mohammad_2103_\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_I_Slot2-10_1_9275.d...
2022-01-04 00:58:48 [INFO] - Checking g:\Mohammad_2103_\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_II_Slot2-19_1_9311.d...
2022-01-04 00:58:49 [INFO] - Checking g:\Mohammad_2103_\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_III_Slot2-10_1_9331.d...
2022-01-04 00:58:50 [INFO] - Checking g:\Mohammad_2103_\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_I_Slot2-11_1_9279.d...
2022-01-04 00:58:51 [INFO] - Checking g:\Mohammad_2103_\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_II_Slot2-28_1_9314.d...
2022-01-04 00:58:52 [INFO] - Checking g:\Mohammad_2103_\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_III_Slot2-11_1_9335.d...
2022-01-04 00:58:53 [INFO] - Loading g:\Mohammad_2103_\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.d...

Best.

Fengchao

[jd690764]

Oh, ok - that makes sense.

So just to summarize what I think this means - please, correct me if I'm wrong - as long as the .d folders are in the same directory as the mzML files, it's ok to use mzML files produced with scanSumming (with/without ion mobility arrays in the files) for ms1 quantitation and PTMprophet in the pipeline?

Thanks, Janos

On Thu, Jan 20, 2022 at 1:10 PM Fengchao @.***> wrote:

Hmm, IonQuant detected that there were .d folders and was using them for quantification. This is actually a feasible workaround.

2022-01-04 00:58:26 [INFO] - Checking g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.d... 2022-01-04 00:58:28 [INFO] - Checking g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_Cep164KO_II_Slot2-20_1_9317.d... 2022-01-04 00:58:29 [INFO] - Checking g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_III_Slot2-12_1_9339.d... 2022-01-04 00:58:31 [INFO] - Checking g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_I_Slot2-13_1_9287.d... 2022-01-04 00:58:32 [INFO] - Checking g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_II_Slot2-29_1_9320.d... 2022-01-04 00:58:34 [INFO] - Checking g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_Cep164KO_III_Slot2-13_1_9343.d... 2022-01-04 00:58:35 [INFO] - Checking g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-23_1_9305.d... 2022-01-04 00:58:36 [INFO] - Checking g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2K50A_I_Slot2-32_1_9308.d... 2022-01-04 00:58:37 [INFO] - Checking g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_I_Slot2-14_1_9291.d... 2022-01-04 00:58:38 [INFO] - Checking g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_II_Slot2-21_1_9325.d... 2022-01-04 00:58:40 [INFO] - Checking g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_III_Slot2-14_1_9347.d... 2022-01-04 00:58:41 [INFO] - Checking g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_I_Slot2-15_1_9295.d... 2022-01-04 00:58:42 [INFO] - Checking g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_II_Slot2-30_1_9328.d... 2022-01-04 00:58:43 [INFO] - Checking g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_III_Slot2-15_1_9351.d... 2022-01-04 00:58:44 [INFO] - Checking g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-22_1_9299.d... 2022-01-04 00:58:45 [INFO] - Checking g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_TTBK2KO_LPAN-TTBK2_I_Slot2-31_1_9302.d... 2022-01-04 00:58:46 [INFO] - Checking g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE_I_Slot2-10_1_9275.d... 2022-01-04 00:58:48 [INFO] - Checking g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-NTA-100ug-RPE_II_Slot2-19_1_9311.d... 2022-01-04 00:58:49 [INFO] - Checking g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-NTA-100ug-RPE_III_Slot2-10_1_9331.d... 2022-01-04 00:58:50 [INFO] - Checking g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-TiO2-100ug-RPE_I_Slot2-11_1_9279.d... 2022-01-04 00:58:51 [INFO] - Checking g:\Mohammad2103\210908\210909_PepSep_10_0701_IMAC-TiO2-100ug-RPE_II_Slot2-28_1_9314.d... 2022-01-04 00:58:52 [INFO] - Checking g:\Mohammad2103\210908\210910_PepSep_10_0701_IMAC-TiO2-100ug-RPE_III_Slot2-11_1_9335.d... 2022-01-04 00:58:53 [INFO] - Loading g:\Mohammad2103\210908\210908_PepSep_10_0701_IMAC-NTA-100ug-RPE-Cep164KO_I_Slot2-12_1_9283.d...

Best.

Fengchao

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/581#issuecomment-1017930965, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACP7QY45RHT5FW52KUOES5DUXB257ANCNFSM5L7VGG4A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

[fcyu]

That is correct.

Best,

Fengchao

[jd690764]

Great, thank you! Janos

On Thu, Jan 20, 2022 at 1:38 PM Fengchao @.***> wrote:

That is correct.

Best,

Fengchao

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/581#issuecomment-1017950417, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACP7QYY2GURJE7JEPL2NA33UXB6FBANCNFSM5L7VGG4A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>