Hi,
as I understand, when using the rescoring functionality of PROSIT, the submitted msms.txt file must come from a MaxQuant search where only a single RAW-file's been run. I think it is a pity though, because it is not very often it is useful to run a MaxQuant search with only one RAW-file. I hope I don´t sound too negative here, I just want to help out.
The rescoring function would be more useful if it could:
(1) Improve a standard database search where several RAW-files been searched in a quantitative workflow (like LFQ).
(2) Create a deeper and more accurate DDA-based spectral library. In this case, several RAW-files would be set up as fractions of a sample in a MaxQuant search, resulting in a single msms.txt file that could go into the PROSIT rescoring. This is what I would like to use the rescoring for, if possible.
I understand that problems can arise if one tries to rescore a MaxQuant search where RAW-files were acquired with different instrument methods or instruments. That could screw up the CE-calibration. But if all files were acquired on the same instrument, with the same instrument method I don't see why it would be a problem to include several RAW-files in the msms.txt. In many (if not most cases) the RAW-files used in a MaxQuant search are acquired by the same instrument method and instrument. So perhaps, one could just warn users of the rescoring function to not upload a msms.txt file where the RAW-files are not acquired by the same method and/or instrument.
Once again, I hope I didn't sound too pessimistic here. I think the idea of rescoring a MaxQuant search or any other search engine with PROSIT is superb.
Hi,
as I understand, when using the rescoring functionality of PROSIT, the submitted msms.txt file must come from a MaxQuant search where only a single RAW-file's been run. I think it is a pity though, because it is not very often it is useful to run a MaxQuant search with only one RAW-file. I hope I don´t sound too negative here, I just want to help out.
The rescoring function would be more useful if it could:
(1) Improve a standard database search where several RAW-files been searched in a quantitative workflow (like LFQ).
(2) Create a deeper and more accurate DDA-based spectral library. In this case, several RAW-files would be set up as fractions of a sample in a MaxQuant search, resulting in a single msms.txt file that could go into the PROSIT rescoring. This is what I would like to use the rescoring for, if possible.
I understand that problems can arise if one tries to rescore a MaxQuant search where RAW-files were acquired with different instrument methods or instruments. That could screw up the CE-calibration. But if all files were acquired on the same instrument, with the same instrument method I don't see why it would be a problem to include several RAW-files in the msms.txt. In many (if not most cases) the RAW-files used in a MaxQuant search are acquired by the same instrument method and instrument. So perhaps, one could just warn users of the rescoring function to not upload a msms.txt file where the RAW-files are not acquired by the same method and/or instrument.
Once again, I hope I didn't sound too pessimistic here. I think the idea of rescoring a MaxQuant search or any other search engine with PROSIT is superb.