Abstract The Trans‐Proteomic Pipeline (TPP) is a suite of software tools for the analysis of
MS/MS data sets. The tools encompass most of the steps in a proteomic data analysis …

Assembling peptides identified from tandem mass spectra into a list of proteins, referred to
as protein inference, is a critical step in proteomics research. Due to the existence of …

Background The detection of physiologically relevant protein isoforms encoded by the
human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the …

Replicate mass spectrometry (MS) measurements and the use of multiple analytical
methods can greatly expand the comprehensiveness of shotgun proteomic profiling of …

Protein biomarker discovery produces lengthy lists of candidates that must subsequently be
verified in blood or other accessible biofluids. Use of targeted mass spectrometry (MS) to …

Automated database search engines are one of the fundamental engines of high-throughput
proteomics enabling daily identifications of hundreds of thousands of peptides and proteins …

We present a peptide library and data resource of> 100,000 synthetic, unmodified peptides
and their phosphorylated counterparts with known sequences and phosphorylation sites …

Generating top-down tandem mass spectra (MS/MS) from complex mixtures of proteoforms
benefits from improvements in fractionation, separation, fragmentation, and mass analysis …

Mass spectrometry, the core technology in the field of proteomics, promises to enable
scientists to identify and quantify the entire complement of proteins in a complex biological …

With great biological interest in post-translational modifications (PTMs), various approaches
have been introduced to identify PTMs using MS/MS. Recent developments for PTM …