Hello Shagun, Thank you for the detailed report. If you are able, please first compress (into a zip or similar) and then share some of the problem .d files so I can try to replicate this issue on my computer before I offer any suggestions.
Cheers! -David On Tue, Aug 13, 2024 at 7:50 AM Shagun Gupta <[email protected]> wrote: > 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 > <https://groups.google.com/d/msgid/spctools-discuss/cf666974-5c1f-4de0-80ad-d9b1df2173dan%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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/CAGJJY%3D80cbTzjeCA7jSYLUWcXxFo5A3PELSikr4BjmzOVbnp%2Bg%40mail.gmail.com.
