Despite these advances in instrumentation and methodologies, there are few methods that fully exploit the information available from the acidic proteome or acidic regions of proteins.

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This bottom-up approach remains the most popular strategy for protein identification, biomarker discovery, quantitative proteomics, and elucidation of post-translational modifications.

To date, proteome characterization via mass spectrometry has overwhelmingly focused on the analysis of peptide cations (5), resulting in an inherent bias toward basic peptides that easily ionize under acidic mobile phase conditions and positive polarity MS settings.

In this work, we have modified the mass accuracy sensitive probabilistic Mass Matrix algorithms to allow database searching of negative polarity MS/MS spectra.

The algorithm is specific to the fragmentation behavior generated from 193-nm UVPD of peptide anions.

Given that ∼50% of peptides/proteins are naturally acidic (6) and that many of the most important post-translational modifications ( phosphorylation, acetylation, sulfonation, etc.) significantly decrease the isoelectric points of peptides (7, 8), there is a compelling need for better analytical methodologies for characterization of the acidic proteome.

A principal reason for the shortage of methods for peptide anion characterization is the lack of MS/MS techniques suitable for the efficient and predictable dissociation of peptide anions.Mass Matrix (27), a recently introduced searching algorithm, uses a mass accuracy sensitive probability-based scoring scheme for both the total number of matched product ions and the total abundance of matched products.This searching method also utilizes LC retention times to filter false positive peptide matches (28) and has been shown to yield results comparable to or better than those obtained with SEQUEST, MASCOT, OMSSA, and X! Despite the ongoing innovation in automated peptide cation analysis, there is a lack of publically available methods for automated peptide anion analysis.Relative to searching using ETD alone, positive/negative polarity switching significantly improved sequence coverages across identified proteins, resulting in a 33% increase in unique peptide identifications and more than twice the number of peptide spectral matches.The advent of new high-performance tandem mass spectrometers equipped with the most versatile collision- and electron-based activation methods and ever more powerful database search algorithms has catalyzed tremendous progress in the field of proteomics (1–4).Another new technique, negative ETD, entails reactions of radical cation reagents with peptide anions to promote electron transfer from the peptide to the reagent that causes radical-directed dissociation (16, 17).