title: MS-driven protease substrate degradomics.
abstract: Proteolytic processing has recently received increased attention in the field of signal propagation and cellular differentiation. Because of its irreversible nature, protein cleavage has been associated with committed steps in cell function. One aspect of protease biology that boomed the past few years is the detailed characterization of protease substrates by both shotgun as well as targeted MS-driven proteomics techniques. The most promising techniques are discussed in this review and we further elaborate on the bioinformatics challenges that accompany mainly qualitative, MS-driven protease substrate degradome studies.
authors.affiliation: Department of Medical Protein Research, VIB, Ghent, Belgium.
authors.forename: Francis
authors.initials: F
authors.lastname: Impens
authors.forename: Niklaas
authors.initials: N
authors.lastname: Colaert
authors.forename: Kenny
authors.initials: K
authors.lastname: Helsens
authors.forename: Kim
authors.initials: K
authors.lastname: Plasman
authors.forename: Petra
authors.initials: P
authors.lastname: Van Damme
authors.forename: Joël
authors.initials: J
authors.lastname: Vandekerckhove
authors.forename: Kris
authors.initials: K
authors.lastname: Gevaert
mesh_terms: D000595:Amino Acid Sequence; D002852:Chromatography, Ion Exchange; D019295:Computational Biology; D007553:Isotope Labeling / Q000379:methods; D013058:Mass Spectrometry; D055432:Metabolomics; D010446:Peptide Fragments / Q000032:analysis; D010447:Peptide Hydrolases / Q000378:metabolism*; D010453:Peptide Synthases / Q000378:metabolism; D010455:Peptides / Q000302:isolation & purification; D040901:Proteomics / Q000379:methods*; D015398:Signal Transduction; D013379:Substrate Specificity; D013381:Subtilisins / Q000378:metabolism
chemical_list: D010446:Peptide Fragments; D010455:Peptides; D010447:Peptide Hydrolases; D013381:Subtilisins; D010453:Peptide Synthases; C117282:subtiligase