Hello Shagun, I downloaded the larger zip file twice and tried to decompress, but each time it told me there was a corruption in the zip file. The smaller files downloaded fine. Can you check your file and upload again?
Thanks! -David On Tue, Aug 13, 2024 at 9:47 AM Shagun Gupta <[email protected]> wrote: > 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 > <https://groups.google.com/d/msgid/spctools-discuss/21faed8c-1c4d-45b8-a281-f3f572864ed1n%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%3D-ObBuJHptc_b5YJWzmXpLHsEZQYLYX%2Bo-UFB4OkgwKcw%40mail.gmail.com.
