Hello Alex, I was able to download your file, convert the data to mzML using msconvert and read a few spectra using the command line tool readMzXml (works on mzML too). Unfortunately, I am finding many intensities these files that are encoded with negative values, which is likely causing problems for the downstream tools like comet. Do you know why negative intensities are in these files? It is possible this is a bug with the raw encoding. Are you able to visualize these files using Waters software to check the intensities and compare to those output by msconvert?
Thanks, -David > On Jan 5, 2024, at 4:17 AM, Alex Gao <alexkao1...@gmail.com> wrote: > > Hi David, > > Thank you for your prompt feedback! The file can be found at the link below. > > https://drive.google.com/file/d/1QulcwZ3UP7pcMtECNwubd4DysqaDq4UN/view?usp=sharing > > Looking forward to your inputs! > > Best, > Alex > > On Friday, January 5, 2024 at 1:09:03 AM UTC+1 David Shteynberg wrote: >> Hello Alex, >> >> Thanks for trying the TPP pipeline to solve your proteomics computational >> needs. Sorry, you are having trouble converting and analyzing Waters raw >> data. Have you tried using the latest version of msconvert to do the >> conversion to mzML? If you are able to upload your file to an online drive >> and give me access to it, I can pull it down and try to convert it myself. >> Let me know what works for you. >> >> Cheers! >> -David >> >> >>> On Jan 3, 2024, at 4:32 AM, Alex Gao <alexk...@gmail.com <>> wrote: >>> >> >>> Hi guys, >>> >>> So I've used TPP before to convert bottom up proteomic Thermo raw files in >>> msconvert, comet search with custom params file, and xinteract to perform >>> protein prophet with no issues. Earlier this year, I performed the same >>> with Waters. Raw file, although in the beginning there was an issue with >>> size, shrinking the size of my raw file from 25 to 5-6GB did the trick. >>> >>> However, recently, I reinstalled TPP (v6.3.3), and was trying to perform >>> the same task to convert 5-6GB of Waters.raw but failed. msconvert didn't >>> fail, but comet search was finished in less than 1min, which is not quite >>> right. And out of the 200,000 spectra in the original file, only 1000 ish >>> was used for comet search. this obviously leads to an error code of 256 at >>> the xinteract level. >>> >>> I tried several different troubleshoots, not changing the default params >>> file except for location of fasta file, uninstalling and reinstalling, >>> changing a computer, renaming the FUNC0003 files from my Water.raw >>> directory for the search, etc. etc., but none work. >>> >>> Any help would be much appreciated. Thank you! >>> >>> Best, >>> Alex >>> >> >>> -- >>> 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 spctools-discu...@googlegroups.com <>. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/spctools-discuss/84cf1e94-32b3-47f6-80a8-37150ff94d93n%40googlegroups.com >>> >>> <https://groups.google.com/d/msgid/spctools-discuss/84cf1e94-32b3-47f6-80a8-37150ff94d93n%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 spctools-discuss+unsubscr...@googlegroups.com > <mailto:spctools-discuss+unsubscr...@googlegroups.com>. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/d774140c-2641-48f2-b9c7-900442b10503n%40googlegroups.com > > <https://groups.google.com/d/msgid/spctools-discuss/d774140c-2641-48f2-b9c7-900442b10503n%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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/C2AF0EED-928E-4955-A74A-CD578AFEED01%40systemsbiology.org.
