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 10000 spectra batch size to see if I can obtain shorter analysis time.
Thanks, Eslam On Wed, Aug 10, 2016 at 7:54 AM, Jimmy Eng <jke...@gmail.com> wrote: > 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 sizes of 10000. > > On Wed, Aug 10, 2016 at 12:27 AM, Eslam Nouri <eslamno...@gmail.com> > wrote: > >> 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. Database search takes a >> long time, but it identifies a large number of microbiome proteins with >> high confidence. >> >> Eslam >> >> On Tue, Aug 9, 2016 at 11:39 PM, Jimmy Eng <jke...@gmail.com> wrote: >> >>> 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 larger. >>> You can give things up (no variable modifications, no missed cleavages, >>> narrow precursor mass tolerance, etc.) to hopefully speed things up a >>> little bit. Otherwise you just have to throw more horsepower at it. You >>> can get Broadwell-class Xeon processors with up to 24 cores in them. >>> >>> On Tue, Aug 9, 2016 at 11:30 PM, Eslam Nouri <eslamno...@gmail.com> >>> wrote: >>> >>>> Hi Eric, >>>> >>>> I am using comet. In my comet file the number of threads is equal to >>>> zero "num_threads = 0". I have attached my system information. Is >>>> there any way to increase the data analysis time by defining a thread >>>> number? >>>> >>>> Thanks, Eslam >>>> >>>> On Tue, Aug 9, 2016 at 11:18 PM, Eric Deutsch < >>>> edeut...@systemsbiology.org> wrote: >>>> >>>>> 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: >>>>> spctools-discuss@googlegroups.com] *On Behalf Of *Eslam Nouri >>>>> *Sent:* Tuesday, August 9, 2016 11:05 PM >>>>> *To:* spctools-discuss@googlegroups.com >>>>> *Subject:* [spctools-discuss] Multi core analysis >>>>> >>>>> >>>>> >>>>> Hello_ >>>>> >>>>> >>>>> >>>>> I am using TPP for the database search of microbiome proteins. Since >>>>> the fasta file that I have is more than 100 times larger than human >>>>> uniprot >>>>> fasta file, the database search for a single DDA run takes more than 12 >>>>> hours. Is there any way to have faster analysis using multi-cores? >>>>> >>>>> >>>>> >>>>> Thanks, Eslam >>>>> >>>>> Proteomics core facility >>>>> >>>>> University of southern California >>>>> >>>>> -- >>>>> 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 post to this group, send email to spctools-discuss@googlegroups.com >>>>> . >>>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>>> -- >>>>> 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 post to this group, send email to spctools-discuss@googlegroups.com >>>>> . >>>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> -- >>>> 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 post to this group, send email to spctools-discuss@googlegroups.com. >>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >>> 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 post to this group, send email to spctools-discuss@googlegroups.com. >>> Visit this group at https://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- >> 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 post to this group, send email to spctools-discuss@googlegroups.com. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- > 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 post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- 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 post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
