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. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/d774140c-2641-48f2-b9c7-900442b10503n%40googlegroups.com.
