title: Strategies in protein sequencing and characterization: multi-enzyme digestion coupled with alternate CID/ETD tandem mass spectrometry.
abstract: A strategy based on a simultaneous multi-enzyme digestion coupled with electron transfer dissociation (ETD) and collision-induced dissociation (CID) was developed for protein sequencing and characterization, as a valid alternative platform in ion-trap based proteomics. The effect of different proteolytic procedures using chymotrypsin, trypsin, a combination of both, and Lys-C, was carefully evaluated in terms of number of identified peptides, protein coverage, and score distribution. A systematic comparison between CID and ETD is shown for the analysis of peptides originating from the in-solution digestion of standard caseins. The best results were achieved with a trypsin/chymotrypsin mix combined with CID and ETD operating in alternating mode. A post-database search validation of MS/MS dataset was performed, then, the matched peptides were cross checked by the evaluation of ion scores, rank, number of experimental product ions, and their relative abundances in the MS/MS spectrum. By integrated CID/ETD experiments, high quality-spectra have been obtained, thus allowing a confirmation of spectral information and an increase of accuracy in peptide sequence assignments. Overlapping peptides, produced throughout the proteins, reduce the ambiguity in mapping modifications between natural variants and animal species, and allow the characterization of post translational modifications. The advantages of using the enzymatic mix trypsin/chymotrypsin were confirmed by the nanoLC and CID/ETD tandem mass spectrometry of goat milk proteins, previously separated by two-dimensional gel electrophoresis.
authors.affiliation: Dipartimento di Scienze Agrarie, degli Alimenti e dell' Ambiente, Università degli Studi di Foggia, Via Napoli, 25-71122 Foggia, Italy.
authors.forename: Donatella
authors.initials: D
authors.lastname: Nardiello
authors.affiliation: Dipartimento di Scienze Agrarie, degli Alimenti e dell' Ambiente, Università degli Studi di Foggia, Via Napoli, 25-71122 Foggia, Italy. Electronic address: carmen.palermo@unifg.it.
authors.forename: Carmen
authors.initials: C
authors.lastname: Palermo
authors.affiliation: Dipartimento di Scienze Agrarie, degli Alimenti e dell' Ambiente, Università degli Studi di Foggia, Via Napoli, 25-71122 Foggia, Italy.
authors.forename: Anna
authors.initials: A
authors.lastname: Natale
authors.affiliation: Dipartimento di Scienze Agrarie, degli Alimenti e dell' Ambiente, Università degli Studi di Foggia, Via Napoli, 25-71122 Foggia, Italy.
authors.forename: Maurizio
authors.initials: M
authors.lastname: Quinto
authors.affiliation: Dipartimento di Scienze Agrarie, degli Alimenti e dell' Ambiente, Università degli Studi di Foggia, Via Napoli, 25-71122 Foggia, Italy.
authors.forename: Diego
authors.initials: D
authors.lastname: Centonze
mesh_terms: D000818:Animals; D002853:Chromatography, Liquid; D004798:Enzymes / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D004798:Enzymes; D011506:Proteins
keywords: Collision induced dissociation; Electron transfer dissociation; Enzymatic digestion; Post-translational modifications; Sequence variants; Species-specific residues