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Nesvilab
LFQ Phospho search with timsTOF Pro data (converted to mzml with MSConvert)
Dear Sir/Madam, I have being trying to carry out a search of 72 Ti02 phospho- enriched proteomics samples, I have previously tried with 4 and the search worked. I converted the Bruker.d files to mzml (file sizes increase from 1-3 gb to 8-15 gb) I have plenty of space on my drive (approx 1.2 tb). I have pasted the error message and attached the log file, any help would be greatly appreciated. Best Regards Kieran
Hi Kieran,
Thanks for your report. We are working on this issue right now.
In the next release, FragPipe will be able to 1) write a mass calibrated mzML file for .d format so that you no longer need to convert the .d, which is time consuming and the file size is big; and 2) the bug related to the pep.xml.tmp file will be fixed.
Stay tuned.
Best,
Fengchao
Thank's Fengchao, You're quick response is appreciated Kind Regards Kieran
On Fri, 30 Sep 2022, 18:53 Fengchao, @.***> wrote:
Hi Kieran,
Thanks for your report. We are working on this issue right now.
In the next release, FragPipe will be able to 1) write a mass calibrated mzML file for .d format so that you no longer need to convert the .d, which is time consuming and the file size is big; and 2) the bug related to the pep.xml.tmp file will be fixed.
Stay tuned.
Best,
Fengchao
— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/846#issuecomment-1263854582, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUPV2DW76EPS6B4K7F37AZLWA4SH3ANCNFSM6AAAAAAQZ7E3Z4 . You are receiving this because you authored the thread.Message ID: @.***>
We have the pre-release versions of FragPipe and MSFragger than can 1) Fix the multi-threading issue in PTMProphet; and 2) support timsTOF .d raw data for the phospho and other PTM analysis that need PTMProphet.
Please contact us for the pre-release versions if you want to have a try.
Best,
Fengchao
Hi Fengchao, Is this the pre-release versions you sent me last week. I'm not sure if the version you sent me last week can use .d files directly for performing phospho localisation (could I get the new version). Quick question when we use "scan summing when converting timstof data in msconvert it is not suitable for ms1 based quantification. This is obviously a problem for lfq-phospho workflow. Should I omit scan summing from my data conversion and is this rectified in the new version of Fragpipe. Thanks again for your help. Best regards Kieran
On Thu, 27 Oct 2022, 22:17 Fengchao, @.***> wrote:
We have the pre-release versions of FragPipe and MSFragger than can 1) Fix the multi-threading issue in PTMProphet; and 2) support timsTOF .d raw data for the phospho and other PTM analysis that need PTMProphet.
Please contact us for the pre-release versions if you want to have a try.
Best,
Fengchao
— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/846#issuecomment-1294073042, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUPV2DTPKSPYXO4DGW7SDJ3WFLWNRANCNFSM6AAAAAAQZ7E3Z4 . You are receiving this because you authored the thread.Message ID: @.***>
Hi Kieran,
Yes, you should avoid converting .d to mzML using msconvert because the "scan summing" will cause issues for the LFQ.
Please send an email to yufe AT umich.edu so that I can send you the link to the pre-release version of MSFragger. I can't send it here due to the license issue.
Best,
Fengchao