PepWise: Peptide Identification Algorithms for Tandem Mass Spectrometry Based on the Weight of Pair Amino Acid Fracture

Abstract

Tandem mass spectrometry is the core of the high-throughput techniques for protein identification. Abundant of MS/MS data can be generated and need to be interpreted, although numerous of peptide identification algorithms have been proposed, most well-known algorithms have been prevailingly employed to predict fragment m/z value to assign peptide sequences to spectrum, such as X!Tandem, OMSSA, Sequest, SQID and ProVerB incorporate intensity information into algorithms to assist peptide identification. Hence, we can easily know, different algorithms would use different information from the same MS data sets. Here we describe a novel protein algorithm based on the weight of pair amino acid fracture, named PepWise, compared with Mascot, Sequest at 1% False Discovery Rate (FDR), which verified the more accuracy, robustness and compatibility.