Purity shows NA with raw files as input

jmcalist commented 2 years ago

Describe the issue or question: Hello, Thank you for offering wonderful software! We were doing a TMT run and it seems to have stopped with 1 remaining task, with a message of can't find the reference channel. I attached a screenshot with the reference channel labeled as pool in the annotation file, and the Ref sample tag indicated as pool. I am sure I am missing something, please let me know :)

Thanks so much!

All the best,

Jason

Upload your log file log_2021-12-09_12-49-38.txt

(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.) Fragpipe TMT Ref sample pool

prvst commented 2 years ago

Hi Jason, did you run the isobaric quantification step?

jmcalist commented 2 years ago

Hi Felipe,

Thank you so much for your reply! I believe I did, but it is my first time trying TMT with Fragpipe so I may have missed it, does it show up in the logfile?

Thanks again!

All the best,

Jason

From: Felipe da Veiga Leprevost @.> Sent: Thursday, December 9, 2021 3:46 PM To: Nesvilab/FragPipe @.> Cc: Jason Mcalister @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] TMT Ref pool (Issue #559)

CAUTION: This email originated from outside of the University of Guelph. Do not click links or open attachments unless you recognize the sender and know the content is safe. If in doubt, forward suspicious emails to @.***

Hi Jason, did you run the isobaric quantification step?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/559#issuecomment-990237172, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARFTQLLFLV5XNMNUUYKYE73UQEIT3ANCNFSM5JXC6KTQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

prvst commented 2 years ago

It looks like you went from the filter to TMT-Integrator. Why do you give it another shot, make sure you have the TMT quantification checked.

sarah-haynes commented 2 years ago

Hi Jason, we always recommend loading one of the provided workflows (probably TMT16 in this case), then only modifying settings as needed.

jmcalist commented 2 years ago

Thank you both so much! I believed I used the provided workflow for TMT-16, I did not intend to change other settings, any changes would have been unintentional

In the attached screenshots, are these settings correct:

Run TMT integrator is checked
Should Run MS1 Quant be checked?

Felipe, I did not find where to check TMT quantification, if you could send a screenshot I would really appreciate it :)

I did not upload the annotation files in the screenshots, but we have 8 samples, each with 15 TMT labels and one common channel (pool). Would I therefore have 8 different annotation files, each with the names of the 15 samples, and the common channel (pool)

Thank you again for your help, I hope my replies and questions above make sense 🙂

All the best,

Jason

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From: Sarah Haynes @.> Sent: Thursday, December 9, 2021 4:05:46 PM To: Nesvilab/FragPipe @.> Cc: Jason Mcalister @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] TMT Ref pool (Issue #559)

CAUTION: This email originated from outside of the University of Guelph. Do not click links or open attachments unless you recognize the sender and know the content is safe. If in doubt, forward suspicious emails to @.***

Hi Jason, we always recommend loading one of the provided workflows (probably TMT16 in this case), then only modifying settings as needed.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/559#issuecomment-990252530, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARFTQLKR5MJQJULDRHETI4LUQEK2VANCNFSM5JXC6KTQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

sarah-haynes commented 2 years ago

Yes, you'll need an annotation file to specify the sample-channel mappings for each of the 16-plexes (so 8 different annotation.txt files). Here's our tutorial on analyzing multiple TMT plexes: https://fragpipe.nesvilab.org/docs/tutorial_tmt-2plexes.html

Let me know if you have any problems when you re-load the TMT16 workflow & run.

-- Sarah

jmcalist commented 2 years ago

Hi Sarah,

Thank you so much, I will work on setting this up again tomorrow and let you know

Thanks so much for your assistance and patience 🙂

All the best,

Jason

From: Sarah Haynes @.> Sent: Thursday, December 9, 2021 4:38 PM To: Nesvilab/FragPipe @.> Cc: Jason Mcalister @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] TMT Ref pool (Issue #559)

CAUTION: This email originated from outside of the University of Guelph. Do not click links or open attachments unless you recognize the sender and know the content is safe. If in doubt, forward suspicious emails to @.***

Yes, you'll need an annotation file to specify the sample-channel mappings for each of the 16-plexes (so 8 different annotation.txt files). Here's our tutorial on analyzing multiple TMT plexes: https://fragpipe.nesvilab.org/docs/tutorial_tmt-2plexes.html

Let me know if you have any problems when you re-load the TMT16 workflow & run.

-- Sarah

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/559#issuecomment-990294245, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARFTQLIX4MKODVR7GKV5X4DUQEOTZANCNFSM5JXC6KTQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

jmcalist commented 2 years ago

Hi Sarah,

Thank you so much for your assistance, I ran the TMT tutorial with the provided files and it worked great, reached Done in 14 minutes. When I ran it with my files it stops at the TMT Integrator (see attached log file).

I see that the tmt-report file is empty, so I attached the annotation files here as well for each plex to make sure that they are setup properly. These two annotation files are each in separate folders (see screenshot), each of these 2 folders holds raw data and an annotation file for each plex.

I hope this is helpful and makes sense, thank you so much for any help you can provide 🙂

All the best,

Jason

From: Sarah Haynes @.> Sent: Thursday, December 9, 2021 4:38 PM To: Nesvilab/FragPipe @.> Cc: Jason Mcalister @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] TMT Ref pool (Issue #559)

CAUTION: This email originated from outside of the University of Guelph. Do not click links or open attachments unless you recognize the sender and know the content is safe. If in doubt, forward suspicious emails to @.***

Yes, you'll need an annotation file to specify the sample-channel mappings for each of the 16-plexes (so 8 different annotation.txt files). Here's our tutorial on analyzing multiple TMT plexes: https://fragpipe.nesvilab.org/docs/tutorial_tmt-2plexes.html

Let me know if you have any problems when you re-load the TMT16 workflow & run.

-- Sarah

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/559#issuecomment-990294245, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARFTQLIX4MKODVR7GKV5X4DUQEOTZANCNFSM5JXC6KTQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK

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

LCMS files: Experiment/Group: Reid_TMT_AAC_1

D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1.raw DDA Experiment/Group: Reid_TMT_AAC_2
D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2.raw DDA

36 commands to execute: CheckCentroid D:\Fragpipe\fragpipe\jre\bin\java.exe -Xmx3G -cp "D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar;D:\Fragpipe\fragpipe\tools\batmass-io-1.23.6.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1.raw 7 WorkspaceCleanInit [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A] D:\Fragpipe\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx3G D:\Fragpipe\fragpipe\tools\MSFragger-3.4\MSFragger-3.4.jar D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\fragger.params D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1.raw D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2.raw MSFragger move pepxml D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar;/D:/Fragpipe/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1.pepXML D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1.pepXML MSFragger move pin D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar;/D:/Fragpipe/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1.pin D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1.pin MSFragger move pepxml D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar;/D:/Fragpipe/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2.pepXML D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2.pepXML MSFragger move pin D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar;/D:/Fragpipe/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2.pin D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2.pin Percolator [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2] D:\Fragpipe\fragpipe\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms Nov_26_2021_RB_Plant_TMT_2_percolator_target_psms.tsv --decoy-results-psms Nov_26_2021_RB_Plant_TMT_2_percolator_decoy_psms.tsv Nov_26_2021_RB_Plant_TMT_2.pin Percolator [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1] D:\Fragpipe\fragpipe\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms Nov_26_2021_RB_Plant_TMT_1_percolator_target_psms.tsv --decoy-results-psms Nov_26_2021_RB_Plant_TMT_1_percolator_decoy_psms.tsv Nov_26_2021_RB_Plant_TMT_1.pin Percolator: Convert to pepxml [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2] D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Nov_26_2021_RB_Plant_TMT_2.pin Nov_26_2021_RB_Plant_TMT_2 Nov_26_2021_RB_Plant_TMT_2_percolator_target_psms.tsv Nov_26_2021_RB_Plant_TMT_2_percolator_decoy_psms.tsv interact-Nov_26_2021_RB_Plant_TMT_2 DDA Percolator: Delete temp D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2_percolator_target_psms.tsv Percolator: Delete temp D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1] D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Nov_26_2021_RB_Plant_TMT_1.pin Nov_26_2021_RB_Plant_TMT_1 Nov_26_2021_RB_Plant_TMT_1_percolator_target_psms.tsv Nov_26_2021_RB_Plant_TMT_1_percolator_decoy_psms.tsv interact-Nov_26_2021_RB_Plant_TMT_1 DDA Percolator: Delete temp D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1_percolator_target_psms.tsv Percolator: Delete temp D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1_percolator_decoy_psms.tsv ProteinProphet [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\jgeddesmlab\Downloads\2021-12-13-decoys-contam-uniprot-proteomeUP000019116.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\jgeddesmlab\Downloads\2021-12-13-decoys-contam-uniprot-proteomeUP000019116.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\jgeddesmlab\Downloads\2021-12-13-decoys-contam-uniprot-proteomeUP000019116.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC1] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1 --protxml D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\combined.prot.xml --razor PhilosopherFilter [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC2] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2 --protxml D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\combined.prot.xml --razorbin D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1.meta\razor.bin FreeQuant [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe freequant --ptw 0.4 --tol 10 --raw --dir D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_1 FreeQuant [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe freequant --ptw 0.4 --tol 10 --raw --dir D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_2 Quant (Isobaric) [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe labelquant --tol 20 --level 2 --plex 16 --annot D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_1\annotation.txt --brand tmt --raw --dir D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_1 Quant (Isobaric) [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe labelquant --tol 20 --level 2 --plex 16 --annot D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_2\annotation.txt --brand tmt --raw --dir D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_2 PhilosopherReport [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe report WorkspaceClean [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck TmtIntegrator [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A] D:\Fragpipe\fragpipe\jre\bin\java.exe -Xmx3G -cp "D:\Fragpipe\fragpipe\tools\tmt-integrator-3.2.1.jar" TMTIntegrator D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\tmt-integrator-conf.yml D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1\psm.tsv D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2\psm.tsv


Execution order:

    Cmd: [START], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A]
    Cmd: [CheckCentroid], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A]
    Cmd: [MSFragger], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A]
    Cmd: [Percolator], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A]
    Cmd: [ProteinProphet], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A]
    Cmd: [PhilosopherFilter], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A]
    Cmd: [FreeQuant], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A]
    Cmd: [Quant (Isobaric)], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A]
    Cmd: [PhilosopherReport], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A]
    Cmd: [WorkspaceClean], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2]
    Cmd: [WorkspaceClean], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1]
    Cmd: [WorkspaceClean], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A]
    Cmd: [TmtIntegrator], Work dir: [D:\Reid_TMT_(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A]

# FragPipe v17.1ui state cache

crystalc.run-crystalc=false
database.db-path=C\:\\Users\\jgeddesmlab\\Downloads\\2021-12-13-decoys-contam-uniprot-proteome_UP000019116.fasta.fas
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.library=
diann.q-value=0.01
diann.quantification-strategy=0
diann.run-dia-nn=false
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-msfragger=D\:\\Fragpipe\\fragpipe\\tools\\MSFragger-3.4\\MSFragger-3.4.jar
fragpipe-config.bin-philosopher=D\:\\Fragpipe\\fragpipe\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\jgeddesmlab\\AppData\\Local\\Programs\\Python\\Python38-32\\python
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=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=100000
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
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=3
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=false
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=0
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=20
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=-1/0/1/2/3
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.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=134.5
msfragger.misc.fragger.clear-mz-lo=125.5
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=200
msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
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=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 304.207146,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 304.207146,n^,true,1; 229.162930,S,false,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,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_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
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.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --picked --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.9
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.assign_glycans=true
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
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=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
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=
ptmshepherd.prob_dhexY=
ptmshepherd.prob_neuacOx=
ptmshepherd.prob_neugcOx=
ptmshepherd.prob_phosphoOx=
ptmshepherd.prob_regY=
ptmshepherd.prob_sulfoOx=
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=false
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
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=16
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.groupby=0
tmtintegrator.max_pep_prob_thres=0.9
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=1
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=pool
tmtintegrator.run-tmtintegrator=true
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\Reid_TMT_(AAC_MS)\\Reid_TMT_AAC_Fragpipe\\Fragpipe_Output_A
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=7

CheckCentroid D:\Fragpipe\fragpipe\jre\bin\java.exe -Xmx3G -cp "D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar;D:\Fragpipe\fragpipe\tools\batmass-io-1.23.6.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1.raw 7 Process 'CheckCentroid' finished, exit code: 0 Done in 0 ms. WorkspaceCleanInit [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[10:29:08] Executing Workspace v4.1.1
INFO[10:29:08] Removing workspace
WARN[10:29:08] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[10:29:08] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[10:29:08] Executing Workspace v4.1.1
INFO[10:29:08] Creating workspace
INFO[10:29:08] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[10:29:09] Executing Workspace v4.1.1
INFO[10:29:09] Removing workspace
WARN[10:29:09] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[10:29:09] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[10:29:09] Executing Workspace v4.1.1
INFO[10:29:09] Creating workspace
INFO[10:29:09] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[10:29:10] Executing Workspace v4.1.1
INFO[10:29:10] Removing workspace
WARN[10:29:10] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[10:29:10] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[10:29:10] Executing Workspace v4.1.1
INFO[10:29:10] Creating workspace
INFO[10:29:10] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A] D:\Fragpipe\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx3G D:\Fragpipe\fragpipe\tools\MSFragger-3.4\MSFragger-3.4.jar D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\fragger.params D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1.raw D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2.raw MSFragger version MSFragger-3.4 Batmass-IO version 1.23.6 timsdata library version timsdata-2-8-7-1 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 3 GB memory Checking database... Checking spectral files... D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2.raw: Scans = 68834 D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1.raw: Scans = 68049

****MAIN SEARCH**** Checking database... Parameters: num_threads = 7 database_name = C:\Users\jgeddesmlab\Downloads\2021-12-13-decoys-contam-uniprot-proteome_UP000019116.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 = 20.0 fragment_mass_units = 1 calibrate_mass = 0 use_all_mods_in_first_search = false write_calibrated_mgf = 0 isotope_error = -1/0/1/2/3 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 = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR 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 = true override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 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 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_06 = 304.207146 n^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 304.207146 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Number of unique peptides of length 7: 538380 of length 8: 551853 of length 9: 543649 of length 10: 536268 of length 11: 538665 of length 12: 525746 of length 13: 521544 of length 14: 499588 of length 15: 485640 of length 16: 469665 of length 17: 452615 of length 18: 440094 of length 19: 419737 of length 20: 403036 of length 21: 393791 of length 22: 376277 of length 23: 358902 of length 24: 342885 of length 25: 326442 of length 26: 314000 of length 27: 299259 of length 28: 287815 of length 29: 274852 of length 30: 254638 of length 31: 241355 of length 32: 226225 of length 33: 212764 of length 34: 202623 of length 35: 191969 of length 36: 176958 of length 37: 166720 of length 38: 156346 of length 39: 146897 of length 40: 133909 of length 41: 126560 of length 42: 115396 of length 43: 104093 of length 44: 90261 of length 45: 70013 of length 46: 51383 of length 47: 33755 of length 48: 20765 of length 49: 11692 of length 50: 6361 In total 12641386 peptides. Generated 42999706 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.10 Da. 1936443014 fragments to be searched in 24 slices (28.86 GB total) Operating on slice 1 of 24: Fragment index slice generated in 1.45 s

Nov_26_2021_RB_Plant_TMT_1.raw 62.4 s | deisotoping 1.8 s [progress: 68026/68026 (100%) - 9576 spectra/s] 7.1s
Nov_26_2021_RB_Plant_TMT_2.raw 59.8 s | deisotoping 1.2 s [progress: 68812/68812 (100%) - 10650 spectra/s] 6.5s Operating on slice 2 of 24: Fragment index slice generated in 1.06 s
Nov_26_2021_RB_Plant_TMT_1.raw 52.1 s | deisotoping 1.4 s [progress: 68026/68026 (100%) - 10312 spectra/s] 6.6s
Nov_26_2021_RB_Plant_TMT_2.raw 49.9 s | deisotoping 1.3 s [progress: 68812/68812 (100%) - 11881 spectra/s] 5.8s Operating on slice 3 of 24: Fragment index slice generated in 0.94 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.8 s | deisotoping 1.5 s [progress: 68026/68026 (100%) - 13600 spectra/s] 5.0s
Nov_26_2021_RB_Plant_TMT_2.raw 46.3 s | deisotoping 1.7 s [progress: 68812/68812 (100%) - 13050 spectra/s] 5.3s Operating on slice 4 of 24: Fragment index slice generated in 1.07 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.2 s | deisotoping 1.3 s [progress: 68026/68026 (100%) - 15802 spectra/s] 4.3s
Nov_26_2021_RB_Plant_TMT_2.raw 41.2 s | deisotoping 1.3 s [progress: 68812/68812 (100%) - 15540 spectra/s] 4.4s Operating on slice 5 of 24: Fragment index slice generated in 0.87 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.5 s | deisotoping 1.4 s [progress: 68026/68026 (100%) - 15147 spectra/s] 4.5s
Nov_26_2021_RB_Plant_TMT_2.raw 40.5 s | deisotoping 1.4 s [progress: 68812/68812 (100%) - 17302 spectra/s] 4.0s Operating on slice 6 of 24: Fragment index slice generated in 0.87 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.2 s | deisotoping 1.4 s [progress: 68026/68026 (100%) - 18326 spectra/s] 3.7s
Nov_26_2021_RB_Plant_TMT_2.raw 39.6 s | deisotoping 1.4 s [progress: 68812/68812 (100%) - 18458 spectra/s] 3.7s Operating on slice 7 of 24: Fragment index slice generated in 0.91 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.6 s | deisotoping 1.4 s [progress: 68026/68026 (100%) - 18607 spectra/s] 3.7s
Nov_26_2021_RB_Plant_TMT_2.raw 39.0 s | deisotoping 1.3 s [progress: 68812/68812 (100%) - 19992 spectra/s] 3.4s Operating on slice 8 of 24: Fragment index slice generated in 0.88 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.8 s | deisotoping 1.4 s [progress: 68026/68026 (100%) - 20222 spectra/s] 3.4s
Nov_26_2021_RB_Plant_TMT_2.raw 39.4 s | deisotoping 1.4 s [progress: 68812/68812 (100%) - 20802 spectra/s] 3.3s Operating on slice 9 of 24: Fragment index slice generated in 0.93 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.6 s | deisotoping 1.5 s [progress: 68026/68026 (100%) - 18632 spectra/s] 3.7s
Nov_26_2021_RB_Plant_TMT_2.raw 41.8 s | deisotoping 1.3 s [progress: 68812/68812 (100%) - 21639 spectra/s] 3.2s Operating on slice 10 of 24: Fragment index slice generated in 0.88 s
Nov_26_2021_RB_Plant_TMT_1.raw 40.5 s | deisotoping 1.4 s [progress: 68026/68026 (100%) - 19559 spectra/s] 3.5s
Nov_26_2021_RB_Plant_TMT_2.raw 39.4 s | deisotoping 1.3 s [progress: 68812/68812 (100%) - 22298 spectra/s] 3.1s Operating on slice 11 of 24: Fragment index slice generated in 0.86 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.5 s | deisotoping 1.4 s [progress: 68026/68026 (100%) - 21685 spectra/s] 3.1s
Nov_26_2021_RB_Plant_TMT_2.raw 39.4 s | deisotoping 1.3 s [progress: 68812/68812 (100%) - 23122 spectra/s] 3.0s Operating on slice 12 of 24: Fragment index slice generated in 0.96 s
Nov_26_2021_RB_Plant_TMT_1.raw 40.2 s | deisotoping 1.4 s [progress: 68026/68026 (100%) - 20434 spectra/s] 3.3s
Nov_26_2021_RB_Plant_TMT_2.raw 39.5 s | deisotoping 1.5 s [progress: 68812/68812 (100%) - 22342 spectra/s] 3.1s Operating on slice 13 of 24: Fragment index slice generated in 0.89 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.9 s | deisotoping 1.4 s [progress: 68026/68026 (100%) - 23091 spectra/s] 2.9s
Nov_26_2021_RB_Plant_TMT_2.raw 39.9 s | deisotoping 1.4 s [progress: 68812/68812 (100%) - 24221 spectra/s] 2.8s Operating on slice 14 of 24: Fragment index slice generated in 0.94 s
Nov_26_2021_RB_Plant_TMT_1.raw 40.8 s | deisotoping 1.4 s [progress: 68026/68026 (100%) - 23013 spectra/s] 3.0s
Nov_26_2021_RB_Plant_TMT_2.raw 39.8 s | deisotoping 1.4 s [progress: 68812/68812 (100%) - 23542 spectra/s] 2.9s Operating on slice 15 of 24: Fragment index slice generated in 1.01 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.1 s | deisotoping 1.4 s [progress: 68026/68026 (100%) - 23727 spectra/s] 2.9s
Nov_26_2021_RB_Plant_TMT_2.raw 38.8 s | deisotoping 1.4 s [progress: 68812/68812 (100%) - 23302 spectra/s] 3.0s Operating on slice 16 of 24: Fragment index slice generated in 0.89 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.0 s | deisotoping 1.5 s [progress: 68026/68026 (100%) - 23995 spectra/s] 2.8s
Nov_26_2021_RB_Plant_TMT_2.raw 39.6 s | deisotoping 1.4 s [progress: 68812/68812 (100%) - 23014 spectra/s] 3.0s Operating on slice 17 of 24: Fragment index slice generated in 0.93 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.4 s | deisotoping 1.5 s [progress: 68026/68026 (100%) - 24131 spectra/s] 2.8s
Nov_26_2021_RB_Plant_TMT_2.raw 39.6 s | deisotoping 1.3 s [progress: 68812/68812 (100%) - 23786 spectra/s] 2.9s Operating on slice 18 of 24: Fragment index slice generated in 0.95 s
Nov_26_2021_RB_Plant_TMT_1.raw 40.6 s | deisotoping 1.4 s [progress: 68026/68026 (100%) - 23835 spectra/s] 2.9s
Nov_26_2021_RB_Plant_TMT_2.raw 39.6 s | deisotoping 1.4 s [progress: 68812/68812 (100%) - 24102 spectra/s] 2.9s Operating on slice 19 of 24: Fragment index slice generated in 1.09 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.9 s | deisotoping 1.9 s [progress: 68026/68026 (100%) - 22151 spectra/s] 3.1s
Nov_26_2021_RB_Plant_TMT_2.raw 41.5 s | deisotoping 1.3 s [progress: 68812/68812 (100%) - 20646 spectra/s] 3.3s Operating on slice 20 of 24: Fragment index slice generated in 0.89 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.7 s | deisotoping 1.4 s [progress: 68026/68026 (100%) - 23744 spectra/s] 2.9s
Nov_26_2021_RB_Plant_TMT_2.raw 39.5 s | deisotoping 1.5 s [progress: 68812/68812 (100%) - 23177 spectra/s] 3.0s Operating on slice 21 of 24: Fragment index slice generated in 0.87 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.4 s | deisotoping 1.5 s [progress: 68026/68026 (100%) - 23067 spectra/s] 2.9s
Nov_26_2021_RB_Plant_TMT_2.raw 39.4 s | deisotoping 1.6 s [progress: 68812/68812 (100%) - 20474 spectra/s] 3.4s Operating on slice 22 of 24: Fragment index slice generated in 1.11 s
Nov_26_2021_RB_Plant_TMT_1.raw 43.5 s | deisotoping 1.5 s [progress: 68026/68026 (100%) - 25326 spectra/s] 2.7s
Nov_26_2021_RB_Plant_TMT_2.raw 39.4 s | deisotoping 1.5 s [progress: 68812/68812 (100%) - 23827 spectra/s] 2.9s Operating on slice 23 of 24: Fragment index slice generated in 0.92 s
Nov_26_2021_RB_Plant_TMT_1.raw 39.0 s | deisotoping 1.5 s [progress: 68026/68026 (100%) - 22392 spectra/s] 3.0s
Nov_26_2021_RB_Plant_TMT_2.raw 41.8 s | deisotoping 1.4 s [progress: 68812/68812 (100%) - 21817 spectra/s] 3.2s Operating on slice 24 of 24: Fragment index slice generated in 0.94 s
Nov_26_2021_RB_Plant_TMT_1.raw 42.6 s | deisotoping 1.5 s [progress: 68026/68026 (100%) - 22638 spectra/s] 3.0s | postprocessing 10.6 s
Nov_26_2021_RB_Plant_TMT_2.raw 43.4 s | deisotoping 1.4 s [progress: 68812/68812 (100%) - 25373 spectra/s] 2.7s | postprocessing 8.7 s MAIN SEARCH DONE IN 39.028 MIN

*****TOTAL TIME 39.435 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar;/D:/Fragpipe/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1.pepXML D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar;/D:/Fragpipe/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1.pin D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar;/D:/Fragpipe/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2.pepXML D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar;/D:/Fragpipe/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2.pin D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2.pin Process 'MSFragger move pin' finished, exit code: 0 Percolator [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2] D:\Fragpipe\fragpipe\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms Nov_26_2021_RB_Plant_TMT_2_percolator_target_psms.tsv --decoy-results-psms Nov_26_2021_RB_Plant_TMT_2_percolator_decoy_psms.tsv Nov_26_2021_RB_Plant_TMT_2.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll *@.) in the Department of Genome Sciences at the University of Washington. Issued command: D:\Fragpipe\fragpipe\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms Nov_26_2021_RB_Plant_TMT_2_percolator_target_psms.tsv --decoy-results-psms Nov_26_2021_RB_Plant_TMT_2_percolator_decoy_psms.tsv Nov_26_2021_RB_Plant_TMT_2.pin Started Mon Dec 13 11:08:40 2021 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile Nov_26_2021_RB_Plant_TMT_2.pin Features: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc Found 62916 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 50649 positives and 12267 negatives, size ratio=4.12888 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 23005 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 22778 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 22950 training set positives with q<0.01 in that direction. Found 34393 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.871 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 35891 PSMs with q<0.01 Iteration 2: Estimated 36168 PSMs with q<0.01 Iteration 3: Estimated 36260 PSMs with q<0.01 Iteration 4: Estimated 36254 PSMs with q<0.01 Iteration 5: Estimated 36272 PSMs with q<0.01 Iteration 6: Estimated 36285 PSMs with q<0.01 Iteration 7: Estimated 36285 PSMs with q<0.01 Iteration 8: Estimated 36275 PSMs with q<0.01 Iteration 9: Estimated 36273 PSMs with q<0.01 Iteration 10: Estimated 36288 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.1989 -0.2243 -0.3064 retentiontime 0.0000 0.0000 0.0000 rank -0.4861 -0.6013 -0.5573 abs_ppm -0.2054 -0.2895 -0.2961 isotope_errors -1.6408 -1.8011 -2.0982 log10_evalue -0.7398 -1.6281 -0.8930 hyperscore 1.3388 1.6887 1.4936 delta_hyperscore 2.6193 3.6211 3.4742 matched_ion_num -1.0975 -1.1339 -1.3523 complementary_ions 0.1923 0.2503 0.1495 ion_series -0.7457 -1.0626 -0.9195 weighted_average_abs_fragment_ppm -0.3572 -0.2758 -0.2669 peptide_length 0.0000 0.0000 0.0000 ntt -0.0198 -0.0717 -0.0828 nmc 1.5575 2.1196 2.5145 m0 Found 36187 test set PSMs with q<0.01. Selected best-scoring PSM per scan+expMass (target-decoy competition): 50649 target PSMs and 12267 decoy PSMs. Calculating q values. Final list yields 36193 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 8.409 cpu seconds or 9 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1] D:\Fragpipe\fragpipe\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms Nov_26_2021_RB_Plant_TMT_1_percolator_target_psms.tsv --decoy-results-psms Nov_26_2021_RB_Plant_TMT_1_percolator_decoy_psms.tsv Nov_26_2021_RB_Plant_TMT_1.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll @.**) in the Department of Genome Sciences at the University of Washington. Issued command: D:\Fragpipe\fragpipe\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms Nov_26_2021_RB_Plant_TMT_1_percolator_target_psms.tsv --decoy-results-psms Nov_26_2021_RB_Plant_TMT_1_percolator_decoy_psms.tsv Nov_26_2021_RB_Plant_TMT_1.pin Started Mon Dec 13 11:08:50 2021 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile Nov_26_2021_RB_Plant_TMT_1.pin Features: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc Found 62387 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 50211 positives and 12176 negatives, size ratio=4.12377 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 22778 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 22601 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 22637 training set positives with q<0.01 in that direction. Found 33974 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.947 cpu seconds or 1 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 35664 PSMs with q<0.01 Iteration 2: Estimated 35985 PSMs with q<0.01 Iteration 3: Estimated 36002 PSMs with q<0.01 Iteration 4: Estimated 36005 PSMs with q<0.01 Iteration 5: Estimated 35997 PSMs with q<0.01 Iteration 6: Estimated 35979 PSMs with q<0.01 Iteration 7: Estimated 36000 PSMs with q<0.01 Iteration 8: Estimated 35993 PSMs with q<0.01 Iteration 9: Estimated 36001 PSMs with q<0.01 Iteration 10: Estimated 35999 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.2416 -0.2219 -0.1794 retentiontime 0.0000 0.0000 0.0000 rank -0.7831 -0.7095 -0.6866 abs_ppm -0.2406 -0.2172 -0.1996 isotope_errors -1.6803 -1.6345 -1.8025 log10_evalue -1.0276 -0.6506 -0.7422 hyperscore 1.7047 1.4734 1.4753 delta_hyperscore 3.4492 2.6806 2.4862 matched_ion_num -1.3090 -1.0694 -1.0099 complementary_ions 0.2280 0.2592 0.2348 ion_series -1.0963 -0.8972 -0.8305 weighted_average_abs_fragment_ppm -0.4085 -0.2695 -0.3807 peptide_length 0.0000 0.0000 0.0000 ntt -0.0476 -0.0795 -0.0297 nmc 2.1254 2.0221 1.9849 m0 Found 35966 test set PSMs with q<0.01. Selected best-scoring PSM per scan+expMass (target-decoy competition): 50211 target PSMs and 12176 decoy PSMs. Calculating q values. Final list yields 35976 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 8.666 cpu seconds or 8 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2] D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Nov_26_2021_RB_Plant_TMT_2.pin Nov_26_2021_RB_Plant_TMT_2 Nov_26_2021_RB_Plant_TMT_2_percolator_target_psms.tsv Nov_26_2021_RB_Plant_TMT_2_percolator_decoy_psms.tsv interact-Nov_26_2021_RB_Plant_TMT_2 DDA Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2\Nov_26_2021_RB_Plant_TMT_2_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1] D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Nov_26_2021_RB_Plant_TMT_1.pin Nov_26_2021_RB_Plant_TMT_1 Nov_26_2021_RB_Plant_TMT_1_percolator_target_psms.tsv Nov_26_2021_RB_Plant_TMT_1_percolator_decoy_psms.tsv interact-Nov_26_2021_RB_Plant_TMT_1 DDA Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp D:\Fragpipe\fragpipe\jre\bin\java.exe -cp D:\Fragpipe\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1\Nov_26_2021_RB_Plant_TMT_1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 ProteinProphet [Work dir: D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A] D:\Fragpipe\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\filelist_proteinprophet.txt INFO[11:09:08] Executing ProteinProphet v4.1.1
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64)) (no FPKM) (using degen pep info) Reading in D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_1\interact-Nov_26_2021_RB_Plant_TMT_1.pep.xml... ...read in 0 1+, 14475 2+, 16461 3+, 3478 4+, 352 5+, 19 6+, 0 7+ spectra with min prob 0.9

Reading in D:\ReidTMT(AAC_MS)\Reid_TMT_AAC_Fragpipe\Fragpipe_Output_A\Reid_TMT_AAC_2\interact-Nov_26_2021_RB_Plant_TMT_2.pep.xml... ...read in 0 1+, 15544 2+, 15751 3+, 3303 4+, 347 5+, 25 6+, 0 7+ spectra with min prob 0.9

Initializing 44455 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database C:\Users\jgeddesmlab\Downloads\2021-12-13-decoys-contam-uniprot-proteome_UP000019116.fasta.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 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sarah-haynes commented 2 years ago

Hi Jason, can you try adding the attachments again? You could also upload the entire experiment/directory here and I'll try to run it: https://www.dropbox.com/request/8sHqgrr4ArC2oh2SuL6G

jmcalist commented 2 years ago

Thanks Sarah, here are the attachments, I had sent the last message through our University email (Outlook) and so the attachments may not have made it to you, hopefully these work

I will also upload the files, thank you so much for the offer to run it, very kind!

log_2021-12-13_11-34-55.txt annotation.txt annotation.txt Screenshot 2021-12-14 101558

jmcalist commented 2 years ago

Hi Sarah,

Thank you again for all of your assistance, we really appreciate it!

If I can provide any other information please let me know, I will do my best to get you anything else you need

Thanks so much!

Jason

sarah-haynes commented 2 years ago

Hi Jason, I can indeed reproduce the issue, we are looking into it. Thanks for your patience!

--Sarah

sarah-haynes commented 2 years ago

Hi Jason, could you try converting your files to mzML for the time being? We think there may be something with the .raw files that is causing an issue with the purity calculation, we will investigate further, but please let me know if that works for you in the mean time.

jmcalist commented 2 years ago

Hi Sarah,

Yes, I can certainly do that, thank you so much for all of your assistance! This team's prompt responses helping users with your software is a massive advantage of Fragpipe!

Thanks again to you all and have a happy and safe Holiday Season!

fcyu commented 2 years ago

Close this issue because Philosopher no longer supports raw files.

Nesvilab / FragPipe

Purity shows NA with raw files as input #559