Shotgun proteomics in neuroscience

Abstract

Mass spectrometry-based proteomics is increasingly used to address basic and clinical questions in biomedical research through studies of differential protein expression, protein-protein interactions, and posttranslational modifications. The complex structural and functional organization of the human brain warrants the application of high-throughput, systematic approaches to understand the functional alterations under normal physiological conditions and the perturbations of neurological diseases. This primer focuses on shotgun-proteomics-based tandem mass spectrometry for the identification of proteins in a complex mixture. It describes the basic concepts of protein differential expression analysis and posttranslational modification analysis and discusses several strategies to improve the coverage of the proteome.

Figure 1

Overall strategy of shotgun proteomics. Tissues or cells are first fractionated, and then the proteins are solubilized. The protein solution is digested with a protease, usually trypsin, into peptides. The digest is fractionated to reduce the complexity. While the peptides are eluted from a liquid chromatography column, they are ionized into the mass spectrometer, and their mass is determined by a MS¹ scan. Ions are further selected based on their relative abundance for fragmentation, and a MS² scan records the masses of the fragmentation ions. The MS² spectrum is searched against a protein database using a cluster of computers running in parallel to determine the peptide sequence and then to identify the protein.

Figure 2

Tandem mass spectrometry. A, Schematic representation of a tandem mass spectrometer that operates using tandem by space, typical of triple-quadrupole mass spectrometer. The m/z of the ions is determined while they are passing through the first mass analyzer. Ions of a narrow mass window (e.g. +/- 0.5 amu) are selected to pass through the second quadrupole for collision-induced dissociation (CID), while other ions are rejected. Ions selected for CID are termed precursor ions. While the precursor ions are passing through the collision cell, they collide with an inert gas to induce peptide bond cleavage producing N- and C- terminal fragmentation ion series differing by one amino acid residue. The m/z values of ion series allow the deduction of peptide sequence. B, A MS¹ spectrum is shown on the left. The ion species with an m/z of 731.77 was selected for CID. The resulting MS² spectrum for this precursor ion is shown on the right. Above the MS² spectra is the annotated fragmentation ion series. Fragments containing the C-terminus are denoted as y-ions with the C-terminus termed y1 and the C-terminus plus the next residue termed y2, and so forth. Fragments containing the N-terminus are denoted as b-ions. The m/z difference between the b- or y- ions is the residue mass of an amino acid. In both spectra, the x-axis is the m/z ratio, and the y-axis is the relative abundance.

Figure 3

Multidimensional Protein Identification Technology (MudPIT). A, Peptides are pressure loaded onto a microcapillary column containing RP resin called the loading column followed by the analytical column containing SCX resin connected in tandem with RP resin filling the column to the 5um tip. B, Schematic of the two-dimensional liquid chromatography protocol. First, the peptides are eluted to SCX resin upon running ACN through the column. Next, increasing concentrations of salt “bumps” are applied to the column each followed by an increasing gradient of ACN. Each salt bump displaces a discrete portion of peptides from the SCX, and then is separated by the RP in the analytical column. As the peptides are eluted from the column, they are ionized by ESI and directed into the mass spectrometer.

Figure 4

Quantitation with stable isotopes. A, A protein sample was mixed with an identical sample except the proteins were labeled with ¹⁵N. The ¹⁴N /¹⁵N mixture was then digested, and analyzed on a LIT mass spectrometer. In the MS¹ spectrum, two abundant ¹⁴N peptides (630.52 and 944.86) are observed with the corresponding ¹⁵N peptides (638.35 and 958.75). The x-axis is the m/z ratio and the y-axis is the relative abundance B, Comparison of different strategies to quantify shotgun proteomics experiments. In label-free methods, sample one (S1) and sample two (S2) are never mixed, allowing systematic errors in quantitation to arise from the numerous preparation steps. Metabolic labeling allows the mixt of samples at the earliest step in analysis, eliminating variation in sample preparation, while in vitro labeling strategies, such as ICAT and iTRAQ, control for some, but not all, possible systematic errors.

Figure 5

Analysis of protein phosphorylation. Similar to shotgun analysis of unmodified proteins, phosphoproteins are digested with trypsin. The addition of a phosphate group on a serine, threonine or tyrosine residues in a peptide results in an addition of mass 79.9663 amu on the peptide precursor ions. As shown in the MS¹ spectra, the precursor ion 550.24 is the charge 2 ion of the peptide MPFQADPGGK (m/z 510.25) containing a phosphate group, which can be further identified through MS/MS.