Hi all I have been experiencing issues processing .d files obtained from a Bruker timsTOF HT in DDA-LFQ mode, more specifically getting quantification - precursor intensity - per spectra. I am using TPP V6.3.3 Arcus on a windows computer.
Details - There are 12 .d files (4 repeats of 3 conditions) composed of a human with yeast proteome spike in at different ratios. - Converted to .mzXML using msconvert - Searched with COMET and a search database taken from UniProt for Homo sapiens+Yeast - Processed with PeptideProphet (filtered at probability associated with 1% FDR), XPRESS, ProteinProphet. Ran with -PREC flag (PeptideProphet), -i flag (XPRESS) - Want to do hypothesis testing (comparing the three conditions pairwise) using MSstats. So require raw precursor intensity values to make a file that can be used as input to MSstats. Unfortunately after trying the above, and a few more things, while I get a large number of PSMs passing FDR (~30k), a large proportion of them do not have any precursor intensity value (<1k have some "light area" values). Using the "light area" values also does not give expected results (its a benchmarking dataset and processing with MSFragger gave excellent results that align with expected ratios etc.). Could you suggest things I could be doing differently to get the right results? (I imagine it might have something to do with the initial conversion to mzXML itself?) Happy to share any other details needed! Best Shagun -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/cf666974-5c1f-4de0-80ad-d9b1df2173dan%40googlegroups.com.
