I’m thinking that a very large mzXML file with “UDMSE” in it might be DIA data, and thus Comet is not the right tool? Could this be MS^e data instead of DDA data?
*From:* spctools-discuss@googlegroups.com <spctools-discuss@googlegroups.com> *On Behalf Of *Jason Winget *Sent:* Friday, September 17, 2021 10:02 AM *To:* spctools-discuss <spctools-discuss@googlegroups.com> *Subject:* [spctools-discuss] Re: Max input file size limit for comet search? Hi Steven, what do your comet parameters look like? I'm not sure if this is the problem, but for files with many scans it is good to set the `spectrum_batch_size` parameter to something reasonable, like 10000. The instructions are found in the "fragment ions" comments section of the default parameters file. On Friday, September 17, 2021 at 1:58:10 AM UTC-4 steven...@gmail.com wrote: Hi, I'm a fairly new user to TPP and this sort of analysis in general and had a question about input file sizes during Comet Search. I have downloaded some MS data from a publication via an online database in .mzXML format (the .raw files weren't provided) and have been trying to run a peptide database search using the Comet software with the default param settings. However I consistently get the message "Warning - no spectra searched" and no output file is created (screenshot attached). The mzXML file itself is actually quite large (~26GB) and I was wondering if the size of the input file itself might be the issue? In the case where the input files would be quite large, is there a potential workaround? Apololgies if I've left out any critical information here Thanks in advance, Steven -- 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/ccbb39b3-f5f8-4702-a0dd-587633ac7b2an%40googlegroups.com <https://groups.google.com/d/msgid/spctools-discuss/ccbb39b3-f5f8-4702-a0dd-587633ac7b2an%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/f1ae837ef6e24d8f041474725ab86e19%40mail.gmail.com.
