Biomedical Engineering Reference
In-Depth Information
Chapter 4
Bioinformatics for LC-MS/MS-Based Proteomics
Richard J. Jacob
Abstract
Mass spectrometry instrumentation has continued to develop rapidly in the last two decades, enabled in
part by advances in microelectronic hardware controllers and computerized control and data acquisition
systems. The wealth and complexity of data produced by a modern instrument is such that the data can no
longer be analyzed manually. Computerized data analysis has become
de rigueur
and the bioinformatics
field has expanded to provide software applications for all aspects of the data analysis needed by LC-
MS/MS. The bioinformatics field is evolving rapidly and software applications are continually being
improved or replaced for existing applications as well as developed to support new types of experiments
and analysis enabled by modern instrumentation. Entire topics have been written on MS data analysis
in proteomics but this review will be necessarily brief. In this chapter we will review the bioinformatics
software applications available for different LC-MS/MS analysis tasks.
Key words:
Proteomics, bioinformatics, database searching.
1.
Introduction
Before the advent of genomic databases and modern MS instru-
ments, sequences could only be obtained from MS/MS of highly
abundant endogenous peptides and proteins and the sequenc-
ing techniques were manual and slow. All the data analyses were
done by de novo sequencing of MS/MS spectra. It was rare
that a complete sequence of a peptide could be determined from
an MS/MS spectrum. The first computer programs for protein
and peptide analyses were written to aid in the interpretation of
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