Democratization of genomics technologies has enabled the rapid determination of
genotypes. More recently the democratization of comprehensive proteomics technologies is …

Over the past decade, a series of experimental strategies for mass spectrometry based
quantitative proteomics and corresponding computational methodology for the processing of …

Protein quantification without isotopic labels has been a long-standing interest in the
proteomics field. However, accurate and robust proteome-wide quantification with label-free …

Active neurons exert a mitogenic effect on normal neural precursor and oligodendroglial
precursor cells, the putative cellular origins of high-grade glioma (HGG). By using …

A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in
sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel …

The ProteoWizard software project provides a modular and extensible set of open-source,
cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries …

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 …

This manuscript provides a comprehensive review of the peptide and protein identification
process using tandem mass spectrometry (MS/MS) data generated in shotgun proteomic …

The Comet database search software was initially released as an open source project in late
2012. Prior to that, Comet existed as the University of Washington's academic version of the …

The evolution of mass spectrometry–based proteomic technologies has advanced our
understanding of the complex and dynamic nature of proteomes while concurrently …