[spctools-discuss] Why not run Analyze Proteins when sample label by iTRAQ

Hi everyone I use TPP v4.2 JETSTREAM rev 1, Build 200904071723 to analyse the sample which when label by iTRAQ but the Analyze Protein can't normal finish. The error report is following: running: "C:/Inetpub/tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ ISB/data/LiuXiaoHui/interact.pep.xml"

[spctools-discuss] Combine Search Results

Hi, I got a list of the search results which used different search parameters, I already run InteractParser and PeptideProphetParser on each of them. Is there an easy way to merge individual pep.xml into one pep.xml file and with the hits ranked by peptide prophet? Thanks, Ping --~--~-~

[spctools-discuss] Re: iProphet Information

Hi Bernt, This was only an example. In my work I organise my searches in different directories. This is not the only way this tool can be run. What you suggest is an acceptable alternative. -David On Sun, Jul 12, 2009 at 11:38 PM, Bernt wrote: > > Hi David, > > With reference to the iProphet

[spctools-discuss] Re: PepXML and ProtXML file format documentation + examples

The schemas should, in theory, be self documenting. That's not always as true as it should be, but have you had a careful look at them? -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Zia Khan Sent: Sunday, July 12, 200

[spctools-discuss] error rate corresponding with peptide probability

Hello Does anyone know whether, or not, there is a way to get a list of error rates by 0.001 corresponding with minimum peptide probability on Peptideprophet? For example Errorminimum Peptideprophet 0.001 0.XX 0.002 0.XXX 0.003 0.XX 0.004 0.XXX 0.005 0.XXX --- Thanks, violet --~

[spctools-discuss] Re: iProphet Information

Hi David, With reference to the iProphet usage, as described in your post: InterProphetParser exp1/sequest/interact.pep.xml exp1/xtandem/ interact.pep.xml exp1/mascot/interact.pep.xml exp2/sequest/ interact.pep.xml Do the pepxml files for the different search results (i.e from mascot and xtande

[spctools-discuss] Re: Spectra viewing problem

Hi Jimmy, You are right, the appended index no. is indeed interfering. It's now working and i think all the associated files (.mzXML ; .mgf ; .dat ; .tgz ; .pep.xml) should all have the same filenames. It's not sufficient just to ensure that the filepaths are consistent. I don't know how the tgz

[spctools-discuss] error rate corresponding peptide probability

Hello, I was wondering if there is any way to see a list of error rate by 0.001 corresponding with peptide probability on peptideprophet, or not. For example, Error Min Peptide Probaility 0.001 0.99 0.002 0.XX 0.003 0.XXX 0.004 0.XX 0.005 0.XX --- --- Thanks, violet