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

The proteome refers to the collection of proteins in a given biological organism or system
under a particular set of environmental conditions. The study of proteins, referred to as …

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 …

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 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 …

A major goal of proteomics research is the accurate and sensitive identification and
quantification of a broad range of proteins within a sample. Data-independent acquisition …

Graft-versus-host disease (GVHD), the major complication of allogeneic bone marrow
transplantation, affects the skin, liver, and gastrointestinal tract. There are no plasma …

Background Modern data generation techniques used in distributed systems biology
research projects often create datasets of enormous size and diversity. We argue that in …

Data processing is a central and critical component of a successful proteomics experiment,
and is often the most time-consuming step. There have been considerable advances in the …

Background Broad-based collaborations are becoming increasingly common among
disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary …