huiyinc
commented
2 years ago Hi Sergio,
I have checked your results and the PSMs identified by MSFragger are also shown in the PD results (as the figure shown below). [image: image.png]
Regarding the warning message, MSFragger node indeed performs the search using target and decoy databases, so you don't have to worry that the decoy search is missing. You still might get the warning message even only using MSFragger. I understand that the warning message might be a little misleading, but sorry I currently have no idea how to disable it because the API of PD v2.5 is slightly different from PD v2.4. Thanks.
Huiyin
sciordia @.***> 於 2021年9月28日 週二 下午9:53寫道：
Hi, We have bought a workstation with Windows X and we have installed PD 2.5.0.400 together with the 4 engines we use: Sequest, Mascot, MsAmanda and MsFragger.
I am writing to you because until now we were using this same workflow (both to identify and to quantify) without problems on another computer with PD 2.4 but with the new installation (on the workstation) and PD 2.5 we have problems with the MsFragger node (v3.3).
If we use that search engine (alone or with the other 3 engines), the search ends but with "warnings" in the job queue. The warning says "Peptide Validator: Warning: No decoy search was performed for the following search nodes: - MSFragger (A4) in workflow Workflow. FDR + fixed threshold validation is used instead."
Could you help us to solve the problem, please?. We don't know if it is a PD or MsFragger bug.
We have even tried MsFragger with the default processing and consensus methods that come with MsFragger and the same warning still appears.
I attach the bug report, the project ( *.MSF) and the rawdata used in case you want to try to reproduce the error in this link:
LINK: https://drive.google.com/drive/folders/10saT10Xzu23DvhuOHgYC3u98RKxXG_MT
Thanks for everything.
Best regards, Sergio
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sciordia
Hi, We have bought a workstation with Windows X and we have installed PD 2.5.0.400 together with the 4 engines we use: Sequest, Mascot, MsAmanda and MsFragger.
I am writing to you because until now we were using this same workflow (both to identify and to quantify) without problems on another computer with PD 2.4 but with the new installation (on the workstation) and PD 2.5 we have problems with the MsFragger node (v3.3).
If we use that search engine (alone or with the other 3 engines), the search ends but with "warnings" in the job queue. The warning says "Peptide Validator: Warning: No decoy search was performed for the following search nodes: - MSFragger (A4) in workflow Workflow. FDR + fixed threshold validation is used instead."
Could you help us to solve the problem, please?. We don't know if it is a PD or MsFragger bug.
We have even tried MsFragger with the default processing and consensus methods that come with MsFragger and the same warning still appears.
I attach the bug report, the project ( *.MSF) and the rawdata used in case you want to try to reproduce the error in this link:
LINK: https://drive.google.com/drive/folders/10saT10Xzu23DvhuOHgYC3u98RKxXG_MT
Thanks for everything.
Best regards, Sergio