[spctools-discuss] could not open input file for visualizing LC-MS/MS data using Pepe3D

I am carrying out the TPP Demo 2009 for learning purposes. When I generated the Pep3D image following the tutorial instructions, My results said the the links on images were not active and error could not open input file on both files that were being used. Does anyone know how I can solve thi

Re: [spctools-discuss] which strategy to control false positive for x!tandem?

Dear Amit, I should sort all the spectrum-peptide matching in one raw file by e-value from low to high, than cut the FDR? Am I right? Thank you very much. On Friday, March 29, 2013 12:26:06 PM UTC+8, Amit Kumar Yadav wrote: > > Hi, > > Interpretation of e-values will always be coupled to the da

Re: [spctools-discuss] protein identification FDR

> > Hi Jesse, > > thank you for your answer. I am interested in protein identification (for > now) so it means that I have to estimate FDR for proteins only. I was just > confused because of different information in different papers, now it's clear > (I'd better ask now before presenting resul

Re: [spctools-discuss] could not open input file for visualizing LC-MS/MS data using Pepe3D

Hello Marianne, What version of TPP are you using? Is it a Windows installation? The message that warns about the links being inactive is always displayed whenever there is more than a single mz(X)ML file processed. If files cannot be opened, it means that the file/folder permissions are set too

Re: [spctools-discuss] which strategy to control false positive for x!tandem?

Yes, provided u are using Elias and Gygi method (concatenated search). Regards, *Amit Kumar Yadav * Senior Research Fellow (SRF-CSIR) IGIB, New Delhi (India) *MassWiz Web server* * **MassWiz sourceforge project*