Computational Tandem-Mass Spectrometric protein analysis
Prakash, Savitha S.
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Protein interactions with other proteins, DNA and RNA molecules play an important role in regulating an array of biological processes. Study of such interactions can improve our understanding of the underlying biology. Tandem Mass Spectroscopy (MS) is an effective method for the characterization of proteins since it identifies the molecular weight (m/z) of peptides generated following protein enzymatic digestion. This is possible since in addition to measuring the m/z of the peptide (MS1), this method also measures the m/z of fragmentation products (MS2) generated following collision induced dissociation (CID) of the peptide. In addition, defined homo and hetero-bifunctional chemical cross linking reagents can be used with proteins to determine proximal peptide units that are located at defined distances. Thus, the approximate tertiary structure or the protein and interacting subunits can be determined. Here, we developed a series of computational programs to aid analysis of tandem-MS data for native proteins and for proteins generated following chemical crosslinking. The example case treated in detail is composed of proteins that are crosslinked by a homobifunctional linker called BS3 which links proximal primary amines. The application program is implemented in FORTRAN 90. A web-interface is developed using html coding coupled with Perl scripts on cgi (common gateway interface) platform. The program compares theoretically generated MS1 and MS2 fragment weights with corresponding experimental results of crosslinked protein. Testing of the software is performed using von Willebrand Factor crosslinked with BS3 prior to proteolytic cleavage using trypsin. Results from preliminary analysis of these data are discussed.