In-Gel Microwave-Assisted Acid Hydrolysis of Proteins Combined with Liquid Chromatography Tandem Mass Spectrometry for Mapping Protein Sequences

We report an enabling method for mapping the protein sequence with high sequence coverage. This method combines the high separation power of gel electrophoresis for protein separation with the high sequence coverage capability of microwave-assisted acid hydrolysis (MAAH) mass spectrometry (MS). In-gel MAAH using 25% trifluoroacetic acid was developed and optimized for degrading the gel-separated protein into small peptides suitable for tandem MS sequencing. For bovine serum albumin (BSA) (∼67 kDa), with 4 μg of protein loading onto a gel for separation, followed by excising the protein gel band for in-gel MAAH and then injecting ∼2 μg of the resultant peptides into a liquid chromatography quadrupole time-of-flight mass spectrometer for analysis, 689 ± 54 (<i>n</i> = 3) unique peptides were identified with a protein sequence coverage of 99 ± 1%. Both the number of peptides detected and sequence coverage decreased as the sample amount decreased, mainly due to background interference: 316 ± 59 peptides and 94 ± 3% coverage for 2 μg loading, 136 ± 19 and 76 ± 5% for 1 μg loading, and 30 ± 2 and 32 ± 2% for 0.5 μg loading. To demonstrate the general applicability of the method, 10 gel bands from gel electrophoresis of an albumin-depleted human plasma sample were excised for in-gel MAAH LC-MS analysis. In total, 19 relatively high abundance proteins with molecular weights ranging from ∼8 to ∼160 kD could be mapped with coverage of 100% for six proteins (MW 8759 to 68 425 Da), 96–98% for five proteins (MW 11 458 to 36 431 Da), 92% for three proteins (MW 15 971 to 36 431 Da), 80–87% for four proteins (MW 42 287 to 162 134 Da), and 56% for one protein (MW 51 358 Da). Finally, to demonstrate the applicability of the method for more detailed analysis of complex protein mixtures, two-dimensional (2D) gel electrophoresis was combined with in-gel MAAH, affinity purification, and LC-MS/MS to characterize six bovine alpha-S1-casein phosphoprotein isoforms. Full sequence coverage was achieved for each protein, and six new modification sites were found