CLPM: A Cross-Linked Peptide Mapping Algorithm for Mass Spectrometric Analysis

Background: Protein-protein, protein-DNA and protein-RNA interactions are of central importance in biological systems. Quadrapole Time-of-flight (Q-TOF) mass spectrometry is a sensitive, promising tool for studying these interactions. Combining this technique with chemical crosslinking, it is possible to identify the sites of interactions within these complexes. Due to the complexities of the mass spectrometric data of crosslinked proteins, new software is required to analyze the resulting products of these studies. Result: We designed a Cross-Linked Peptide Mapping (CLPM) algorithm which takes advantage of all of the information available in the experiment including the amino acid sequence from each protein, the identity of the crosslinker, the identity of the digesting enzyme, the level of missed cleavage, and possible chemical modifications. The algorithm does in silico digestion and crosslinking, calculates all possible mass values and matches the theoretical data to the actual ex...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Yong Tang, Yingfeng Chen, Cheryl F. Lichti, Roger A. Hall, Kevin D. Raney, Steven F. Jennings
• Keywords: BMCBI 2005, Mass Spectrometry, Protein-RNA Interactions, Proteins