msmsEval - tandem mass spectral quality assignment for high-throughput proteomics

Tandem mass spectral quality assignment for high-throughput proteomics. The software analyses tandem mass spectral data from peptide LC-MS/MS experiments and empirically assigns a likelihood for the spectrum to be identifiable by peptide MS/MS search engines downstream. It is particularly useful for filtering poor quality spectra and also find high-quality spectrum that are unannotatible by search algorthms and therefore good candidates for representing peptides with post-translational modifications, etc. The source code for msmsEval is avaliable here (msmseval.tbz2). Note that this version now contains a parameter file for Orbitrap/FTICR data.