Thanks for the responses, In the comet parameter file, the 'fragment_bin_tol' value is set to 1.0005 and 'spectrum_batch_size' is set to 15000. I tried running the data using 'spectrum_batch_size' set to 10000 but still had the same issue, which I think Eric has addressed. I will keep in mind to check this setting in future though.
Thanks Eric, I think that was the issue; the data was acquired using a DIA setup and not DDA. I haven't done much work with DIA data before so I will do some reading online and have another crack at it. Thanks again for your responses! On Saturday, September 18, 2021 at 3:11:18 AM UTC+10 Eric Deutsch wrote: > 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:* [email protected] <[email protected]> *On > Behalf Of *Jason Winget > *Sent:* Friday, September 17, 2021 10:02 AM > *To:* spctools-discuss <[email protected]> > *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 [email protected] > 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 [email protected]. > 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/527fb1c3-1e77-42d3-8d12-cf105408a895n%40googlegroups.com.
