Abstract
Mass spectrometry-based identification of the components of multiprotein complexes often involves solution-phase proteolytic digestion of the complex. The affinity purification of individual protein complexes often yields nanogram
to low-microgram amounts of protein, which poses several challenges for enzymatic digestion and protein identification. We tested different solvent systems to optimize trypsin digestions of samples containing limited amounts
of protein for subsequent analysis by LC-MS-MS. Data collected from digestion of 10-, 2-, 1-, and 0.2-�g portions of a protein standard mixture indicated that an organicaqueous solvent system containing 80% acetonitrile consistently
provided the most complete digestion, producing more peptide identifications than the other solvent systems tested. For example, a 1-h digestion in 80% acetonitrile yielded over 52% more peptides than the overnight
digestion of 1 �g of a protein mixture in purely aqueous buffer. This trend was also observed for peptides from digested ribosomal proteins isolated from Rhodopseudomonas palustris. In addition to improved digestion efficiency, the shorter digestion times possible with the organic solvent also improved trypsin specificity, resulting in smaller numbers of semitryptic peptides than an
overnight digestion protocol using an aqueous solvent. The technique was also demonstrated for an affinityisolated protein complex, GroEL. To our knowledge, this report is the first using mass spectrometry data to show a linkage between digestion solvent and trypsin specificity. Mass spectrometry (MS) has become a widely used method for studying proteins, protein complexes, and whole proteomes because of innovations in soft ionization techniques, bioinformatics, and chromatographic separation techniques.1-7 An example of a high-throughput mass spectrometry strategy commonly used for this purpose is a variation of the "shotgun" approach, involving in-solution digestion of a protein complex followed by onedimensional (1D) or two-dimensional (2D) liquid chromatography
(LC) coupled with electrospray ionization (ESI) MS-MS.6-8 One of the applications of this method is for characterizing multiprotein complexes by identifying large numbers of proteins in a single data acquisition.9 Large-scale implementations of this strategy have been reported for yeast and Escherichia coli.10-12 To achieve a goal of characterizing large numbers of protein complexes13 isolated by affinity purification from Rhodopseudomonas palustris,14 an efficient protocol for digesting these complexes is required.