Nowadays, mass spectrometry‐based proteomics is carried out primarily in a bottom‐up
fashion, with peptides obtained after proteolytic digest of a whole proteome lysate as the …

Sequence database search engines are bioinformatics algorithms that identify peptides from
tandem mass spectra using a reference protein sequence database. Two decades of …

Mass spectrometry is unmatched in its versatility for studying practically any aspect of the
proteome. Because the foundations of mass spectrometry-based proteomics are complex …

Protein biomarker discovery produces lengthy lists of candidates that must subsequently be
verified in blood or other accessible biofluids. Use of targeted mass spectrometry (MS) to …

The proteome refers to the collection of proteins in a given biological organism or system
under a particular set of environmental conditions. The study of proteins, referred to as …

Protein identification via peptide mass fingerprinting (PMF) remains a key component of high-
throughput proteomics experiments in post-genomic science. Candidate protein …

A powerful technique for peptide and protein identification is tandem mass spectrometry
followed by database search using a program such as SEQUEST or Mascot. These …

Non-specific proteases are rarely used in quantitative shotgun proteomics due to potentially
high false discovery rates. Yet, there are instances when application of a non-specific …

Trypsin, a high fidelity protease, is the most widely used enzyme for protein digestion in
proteomic research. Optimal digestion conditions are well-known and so are the expected …

Mass spectrometry has served as a major tool for the discipline of proteomics to catalogue
proteins in an unprecedented scale. With chemical and metabolic techniques for stable …