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 <[email protected]> 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 <[email protected]> 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 < >> [email protected]> 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:* [email protected] [mailto:spctools-discuss@googl >>> egroups.com] *On Behalf Of *Eslam Nouri >>> *Sent:* Tuesday, August 9, 2016 11:05 PM >>> *To:* [email protected] >>> *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 [email protected]. >>> To post to this group, send email to [email protected]. >>> 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 [email protected]. >>> To post to this group, send email to [email protected]. >>> 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 [email protected]. >> To post to this group, send email to [email protected]. >> 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 [email protected]. > To post to this group, send email to [email protected]. > 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
