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.


RESULTS
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 experimental data provided by the mass spectrometry analysis to identify the crosslinked peptides.


CONCLUSIONS
Identifying peptides by their masses can be an efficient starting point for direct sequence confirmation. The CLPM algorithm provides a powerful tool in identifying these potential interaction sites in combination with chemical crosslinking and mass spectrometry. Through this cost-effective approach, subsequent efforts can quickly focus attention on investigating these specific interaction sites.
Tang
Yong
Y
Department of Applied Science, University of Arkansas at Little Rock, Little Rock, Arkansas 72204, USA. YxTang2@UALR.edu
Chen
Yingfeng
Y
Lichti
Cheryl F
CF
Hall
Roger A
RA
Raney
Kevin D
KD
Jennings
Steven F
SF
D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D010449:Peptide Mapping / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*