Deep Amino Acid Sequencing of Native Brain GABAA Receptors Using High-Resolution Mass Spectrometry

Mass spectrometric sequencing of low abundance, integral membrane proteins, particularly the transmembrane domains, presents challenges that span the multiple phases of sample preparation including solubilization, purification, enzymatic digestion, peptide extraction, and chromatographic separation. We describe a method through which we have obtained high peptide coverage for 12 gamma-aminobutyric acid type A receptor (GABA(A) receptor) subunits from 2 picomoles of affinity-purified GABA(A) receptors from rat brain neocortex. Focusing on the alpha(1) subunit, we identified peptides covering 96% of the protein sequence from fragmentation spectra (MS2) using a database searching algorithm and deduced 80% of the amino acid residues in the protein from de novo sequencing of Orbitrap spectra. The workflow combined microscale membrane protein solubilization, protein delipidation, in-solution multi-enzyme digestion, multiple stationary phases for peptide extraction, and acquisition of high-resolution full scan and fragmentation spectra. For de novo sequencing of peptides containing the transmembrane domains, timed digestions with chymotrypsin were utilized to generate peptides with overlapping sequences that were then recovered by sequential solid phase extraction using a C4 followed by a porous graphitic carbon stationary phase. The specificity of peptide identifications and amino acid residue sequences was increased by high mass accuracy and charge state assignment to parent and fragment ions. Analysis of three separate brain samples demonstrated that 78% of the sequence of the alpha(1) subunit was observed in all three replicates with an additional 13% covered in two of the three replicates, indicating a high degree of sequence coverage reproducibility. Label-free quantitative analysis was applied to the three replicates to determine the relative abundances of 11 gamma-aminobutyric acid type A receptor subunits. The deep sequence MS data also revealed two N-glycosylation sites on the alpha(1) subunit, confirmed two splice variants of the gamma(2) subunit (gamma(2L) and gamma(2S)) and resolved a database discrepancy in the sequence of the alpha(5) subunit. Molecular & Cellular Proteomics 11: 10.1074/mcp.M111.011445, 1-18, 2012.