Improvement of Shotgun Proteomics in the Negative Mode by Carbamylation of Peptides and Ultraviolet Photodissociation Mass Spectrometry

Although acidic peptides compose a substantial portion of many proteomes, their less efficient ionization during positive polarity electrospray ionization (ESI) impedes their detection in bottom-up mass spectrometry workflows. We have implemented a derivatization strategy based on carbamylation which converts basic amine sites (Lys, N-termini) to less basic amides for enhanced analysis in the negative mode. Ultraviolet photodissociation (UVPD) is used to analyze the resulting peptide anions, as demonstrated for tryptic peptides from bovine serum albumin and Halobacterium salinarum in a high throughput liquid chromatography/tandem mass spectrometry (LC/MS/MS) mode. LC/UVPD-MS of a carbamylated H. salinarum digest resulted in 45% more identified peptides and 25% more proteins compared to the unmodified digest analyzed in the negative mode.