Re: [spctools-discuss] Multi core analysis

If you're running low-res searches (i.e. fragment_bin_size = 1.0005) then you can probably afford to set this value even higher. Just try starting a search and keeping an eye on memory use. As soon as each batch of spectra is loaded and being searched against the sequence database, that should

Re: [spctools-discuss] Multi core analysis

Hi Jimmy, Thanks a lot for the recommendation. I changed the spectra batch size from 1000 to 5000 and could analyze the same DDA sample with 50% improvement in the analysis time. I will surely check the 1 spectra batch size to see if I can obtain shorter analysis time. Thanks, Eslam On Wed,

RE: [spctools-discuss] pepXML: aminoacid_modification elements in search_summary

I don’t require them in my software that reads pepXML because I don’t find these tags reliable, specifically in cases where they are missing. Like SpectraST, Kojak doesn’t export these either. Cheers, Mike From: spctools-discuss@googlegroups.com [mailto:spctools-discuss@googlegroups.com]

[spctools-discuss] pepXML: aminoacid_modification elements in search_summary

Hi everyone, I have a question about use of some pepXML tags. It’s a bit technical and mostly for other developers who use the pepXML format. The issue involves the amino_acid tags at the top of a pepXML file under search_summary, like this: Comet and some other

Re: [spctools-discuss] Multi core analysis

Hi Eslam, Along the lines of what Jimmy mentioned about "giving things up" specifying fully versus partial tryptic really speeds up the search if that is suitable for your sample. I would recommend talking to your IT department to see if they have any ready solutions for increasing your

Re: [spctools-discuss] Multi core analysis

How much memory/RAM do you have on your computer? It won't make a huge difference but larger spectrum batch sizes are more efficient. So see if you have enough free memory to run with that parameter set at say 5000. With our 16GB linux computers performing high-res ms/ms searches, I use batch

Re: [spctools-discuss] Multi core analysis

Thanks a lot Jimmy. It is a relief to know that I am doing the best that I can do with my current system. I have already removed all the dynamic modifications that I had (no methionine oxidation or phosphorylations were defined). I have also confined the analysis to 1000 spectra batch size.

Re: [spctools-discuss] Multi core analysis

Eslam, Setting "num_threads = 0" is the best you can do. There's no free lunch ... a database that's 100 times larger than the human UniProt fasta will take approximately 100 times longer to run, e.g. a 10 minute human search would translate to a 17 hour search if the database were 100 times

RE: [spctools-discuss] Multi core analysis

Which search engine are you using? Comet? Tandem? Comet has num_threads: http://comet-ms.sourceforge.net/parameters/parameters_201601/num_threads.php Tandem has threads: http://www.thegpm.org/TANDEM/api/st.html *From:* spctools-discuss@googlegroups.com [mailto: