[spctools-discuss] ETD Search

Dear All, I want to know about some ETD search tools, preferably free/open-source. I tried Mascot, OMSSA and pFIND but getting drastically different results.Don't know what to believe. X!Tandem TORNADO download page says that they have incorporated ETD search citing pFind's latest paper (JPR,2

[spctools-discuss] Getting Scan IDs from Proteome Discoverer after sequest search

Hi All, Can anyone guide me how to get the spectra IDs(scan IDs) from a Sequest search through proteome discoverer 1.1. I am searching mgf files in sequest and mascot. I get scan IDs in Mascot results exported as csv. Proteome Disoverer allows Sequest results to be exported as excel sheet but i

[spctools-discuss] Is TPP incompatible with Perl 5.12 ?

I have installed Perl 5.12.1 from Activestate. I tried installing TPP4.3 rev1 but it pauses with following error message- "Perl installation/path configuration did not complete" Is TPP incompatible with perl 5.12.1 ? How can I avoid installing Perl 5.10? In other words, is there a way to get TPP

[spctools-discuss] Problem searching with OMSSA

Dear Group Members, I am new to OMSSA. I had an mzXML which i converted to mgf (using mzXML2search.exe).When I exported OMSSA results as CSV files for target - decoy searches, i was puzzled to see same scan ID repeated multiple times (without any rank). I also observed that OMSSA assigned same pep

[spctools-discuss] SpectraST Help

Hi All, I want to use spectraST for spectral library creation and subsequent searches in this spectral library. I have never used it before, am i on the right track? Are there other tools available which can accomplish this for me? How does spec lib search occur(as opposed to database search) ? Ho

[spctools-discuss] PeptideProphet for X!Tandem

Dear All, I was just browsing the gpm site and reading about tandem. It says that peptideprophet and proteinprophet need not be used with X!Tandem. Can someone explain (in simple terms please) how TPP uses tandem result data to assign probabilities? Another naive question is about calculation of

[spctools-discuss] Converting .RAW files

Dear All, I want to try the cpan module "Xcalibur::Rawfile" to convert RAW files to mzXML/mgf/PKL. Has anyone tried it? How does it work ? Do i need Xcalibur SDK on the machine(windows vista home premium)? -- You received this message because you are subscribed to the Google Groups "spctools-d

[spctools-discuss] t2D converter

Hi All, Does anyone know of a .t2D to MzXML/PKL/DTA converter for t2D files from ABI-MALDI TOF/TOF (4700/4800/5800)series MS instruments? I know of one java utility from proteomecommons.org named "ConvertPeakList.jnlp" but it seems to have many bugs. It doesnt convert into PKL/DTA correctly but co

[spctools-discuss] Re: Can PeptideProphet be used with any algorithm?

Hi, I wanted to know if i need to report only the peptide scores or scores with p-and/e-value. On Dec 2, 12:18 pm, Amit Kumar Yadav wrote: > I have never used TPP before, though i have known about it. > I am not using any software on a regular basis. I just use them for > benchmarki

[spctools-discuss] Re: Can PeptideProphet be used with any algorithm?

file and the search scores that are > appropriate and we will work with you to resolve any pepXML issues you > might have and retool the TPP to process your data. > > -David > > On Tue, Dec 1, 2009 at 2:46 AM, Amit Kumar Yadav > > > > wrote: > > Hi, > > >

[spctools-discuss] Can PeptideProphet be used with any algorithm?

Hi, Can we use Peptide Prophet with any algorithm for which we have the APIs? We have developed a new scoring algorithm. Can we use Peptide Prophet with it? If yes, how? What do we need to do so as to incorporate it. Please give details. Thanks in advance- AKY -- You received this message be