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

Systems biology requires comprehensive data at all molecular levels. Mass spectrometry
(MS)-based proteomics has emerged as a powerful and universal method for the global …

A major goal in natural product discovery programs is to rapidly dereplicate known entities
from complex biological extracts. We demonstrate here that molecular networking, an …

Since its introduction, the orbitrap has proven to be a robust mass analyzer that can routinely
deliver high resolving power and mass accuracy. Unlike conventional ion traps such as the …

Cyanotoxins called microcystins (MCs) are highly toxic and can be present in drinking water
sources. Determining the structure of MCs is paramount because of its effect on toxicity …

The success of cancer immunotherapy relies on the ability of cytotoxic T cells to specifically
recognize and eliminate tumor cells based on peptides presented by HLA-I. Although the …

We have characterized the phosphoproteome of Arabidopsis (Arabidopsis thaliana)
seedlings using high-accuracy mass spectrometry and report the identification of 1,429 …

Discovering the gene expression signature associated with a cellular state is one of the
basic quests in majority of biological studies. For most of the clinical and cellular …

A key problem in computational proteomics is distinguishing between correct and false
peptide identifications. We argue that evaluating the error rates of peptide identifications is …

The ultimate goal of proteomics is determination of the exact chemical composition of protein
species, including their complete amino acid sequence and the identification of each …