roteinProphet(TM) automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST. Importantly, it addresses two critical issues: (1) Peptides corresponding to 'single-hit' proteins (those to which no ot...
Byne integrates ByOnic's peptide identifications into a list of proteins, ranked by confidence (p-value). The combination of ByOnic and ComByne greatly outperforms current standards, such as Mascot and ProteinProphet. ByOnic typically identifies 50 to 100 percent more spectra. On comple...
Empirical Bayes Protein identification algorithm. EBP is the first generally applicable protein identification method that can combine the results of multiple search algorithms and replicated LC MS/MS experiments. EBP is compatible with the Trans-Proteomic Pipeline (TPP) from http://sys...