Closed dnwhdals closed 1 year ago
Hi Jongmin,
Can you please check if there is a column, Purity, in your PSM.tsv file? Thanks.
Huiyin
dnwhdals @.***> 於 2021年9月26日 下午2:04 寫道:
Describe the issue or question: Hello, I am struggling with an issue with FragPipe v16.0 while quantifies PSMs in TMT-10 dataset. It seems the tool is not able to generate the "Purity" column in the PSM tables. Please find attached the log file. How can I resolve the issue?
Thank you in advance.
Jongmin Woo
Upload your log file (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. log_2021-09-26_01-54-25.txt ) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.
Hi Jongmin,
I think you didn't run Philosopher' label quant and free quant, which are required by TMT-Integrator. Can you load one of the TMT workflow and try again?
Best,
Fengchao
I tried to re-load TMT10 workflow and re-run the search, but same issue was occurred. In the PSM.tsv file, no "purity" column was created during the process.
Could you more specific of the running Philosopher label quant and free quant? Where can I find the check box of the Philosopher quant?
Hi Jongmin,
Can you send me your log file? Please zip it. Then, drag it to GitHub issue page, or email it to yufe@umich.edu. GitHub somehow won't show the zip attachment if directly replying the email. And GitHub truncates the text file if you attach it directly.
I just tried a dry-run and see those commands in my log, which indicates that freequant and labelquant will be run.
FreeQuant [Work dir: F:\dev\msfragger\dev\exp_1]
C:\Users\yufe\Desktop\bin\philosopher-v4.0.1-RC5.exe freequant --ptw 0.4 --tol 10 --dir E:\data\PXD001468
FreeQuant [Work dir: F:\dev\msfragger\dev\exp_2]
C:\Users\yufe\Desktop\bin\philosopher-v4.0.1-RC5.exe freequant --ptw 0.4 --tol 10 --dir E:\data\PXD001468
FreeQuant [Work dir: F:\dev\msfragger\dev\exp_3]
C:\Users\yufe\Desktop\bin\philosopher-v4.0.1-RC5.exe freequant --ptw 0.4 --tol 10 --dir E:\data\PXD001468
Quant (Isobaric) [Work dir: F:\dev\msfragger\dev\exp]
C:\Users\yufe\Desktop\bin\philosopher-v4.0.1-RC5.exe labelquant --tol 20 --level 2 --plex 10 --annot E:\data\PXD001468\11_annotation.txt --brand tmt --dir E:\data\PXD001468
Best,
Fengchao
Hi Fengchao.
Please find the attached zip file. I can also see the free quant and label quant in a dry run console.
FreeQuant [Work dir: E:\Jacob\NPTDAB_Raw_data\AB01] E:\Jacob\fragpipe\tools\philosopher\philosopher.exe freequant --ptw 0.4 --tol 10 --raw --dir E:\Jacob\NPTDAB_Raw_data Quant (Isobaric) [Work dir: E:\Jacob\NPTDAB_Raw_data\AB01] E:\Jacob\fragpipe\tools\philosopher\philosopher.exe labelquant --tol 20 --level 2 --plex 10 --annot E:\Jacob\NPTDAB_Raw_data\annotation_annotation.txt --brand tmt --raw --dir E:\Jacob\NPTDAB_Raw_data
Best regards, Jongmin
Hi Jongmin,
Thanks for your log. But there is no free quant or label quant in your log. Can you double check?
Best,
Fengchao
log_2021-09-27_13-11-48.zip Could you check out the new log file attached? I uploaded a log file that was created when I first noticed the problem, but strangely there was no labelquant on the log. But if you look at the log file I upload now, you will see that labelquant exists. But I still have the same issue.
Jongmin
Thanks Jongmin,
Yes, the latest log has free quant and label quant, and both of them finished successfully. But TMT-Integer still says that can't find the "Purity" column. Can you help to check if there indeed no "Purity" column in psm.tsv?
Thanks,
Fengchao
No, there is no 'Purity' column on the psm.tsv file. Please take a look the top row of psm file. If you need psm.tsv, I can send you via email because Github doesn't support .tsv file. <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">
Spectrum | Spectrum File | Peptide | Modified Peptide | Prev AA | Next AA | Peptide Length | Charge | Retention | Observed Mass | Calibrated Observed Mass | Observed M/Z | Calibrated Observed M/Z | Calculated Peptide Mass | Calculated M/Z | Delta Mass | Expectation | Hyperscore | Nextscore | PeptideProphet Probability | Number of Enzymatic Termini | Number of Missed Cleavages | Protein Start | Protein End | Intensity | Assigned Modifications | Observed Modifications | Is Unique | Protein | Protein ID | Entry Name | Gene | Protein Description | Mapped Genes | Mapped Proteins | Quan Usage | TP01 | TP02 | TP03 | TP04 | TP05 | TP06 | TP07 | TP08 | TP09 | pool -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | --
I am struggling with an issue with FragPipe v16.0 while quantifies PSMs in TMT-10 dataset. It seems the tool is not able to generate the "Purity" column in the PSM tables. Please find attached the log file. How can I resolve the issue?
Thank you in advance.
Jongmin Woo