Hi David Apologies for the hassle! I have uploaded the .d files in an unzipped format under TPP_diagnosis/TPP_diagnosis. Let me know if this works instead?
Best Shagun On Tuesday, August 13, 2024 at 3:09:37 PM UTC-4 David Shteynberg wrote: > 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/1e530c4b-d879-4117-9708-ae204d2198e5n%40googlegroups.com.
