Hi David I have attached a link to the following files - one replicate per condition .d file (file starting with "C_" had IDs but no values that could be extracted for quantification) - comet parameter file I used - fasta file I ran the search with.
Let me know if I can share anything else! Box_link_diagnosis <https://cornell.box.com/s/5y2uak2twszajaniaqpnevxn4zdneu54> Best Shagun On Tuesday, August 13, 2024 at 11:05:42 AM UTC-4 David Shteynberg wrote: > 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/21faed8c-1c4d-45b8-a281-f3f572864ed1n%40googlegroups.com.
