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 computing power. They may have resources available that you are not aware of. For example, I talked to the IT Dept. here and they happily set up a 12 core virtual machine that I installed TPP on. They would have done more, but ultimately they wanted to charge me a yearly fee and I decided to go the less expensive route and buy pre-owned "pizza boxes" with dual hex cores, install Ubuntu and TPP myself. These are relatively inexpensive on E-Bay for ~$500 depending on configuration. Here is one example: http://www.ebay.com/itm/HP-Proliant-DL360-G7-Server-2x-X5670-2-93GHz-HexaCore-128GB-4x-450GB-2x-power-/322197730383?hash=item4b047b344f:g:FOAAAOSwtnpXpQMR You may be able to work with such companies that sell these units to have them configured to your specs. So the above would be for just one shared memory system with 12 cores (+12 virtual cores if you config it that way since these processors support hyper theading, which may or may not speed things up. Apparently with hyper threading more isn't always better). Using Ubuntu or other Linux distros, you can set up a cluster of many of these inexpensive boxes that will work in parallel to further increase your processing power. With 5 such boxes, mentioned above, you could have a 60 core cluster for less than $3000 in hardware. Ultimately its your budget and ability to do things yourself that will determine what is best for you. Cheers, Brian Brian Hampton Protein Analysis Lab Center for Vascular and Inflammatory Diseases University of Maryland School of Medicine 655 West Baltimore Street BRB 7-018 Baltimore MD 21201 V: 410-706-8207 On Wed, Aug 10, 2016 at 2:05 AM, Eslam Nouri <eslamno...@gmail.com> wrote: > 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.
