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

Automated methods for assigning peptides to observed tandem mass spectra typically return
a list of peptide− spectrum matches, ranked according to an arbitrary score. In this article, we …

Sepsis is a common cause of death, but outcomes in individual patients are difficult to
predict. Elucidating the molecular processes that differ between sepsis patients who survive …

The analysis of the large amount of data generated in mass spectrometry–based proteomics
experiments represents a significant challenge and is currently a bottleneck in many …

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 …

Motivation: A mass spectrum produced via tandem mass spectrometry can be tentatively
matched to a peptide sequence via database search. Here, we address the problem of …

This review is the continuation of three previously published articles [Jorrin JV, Maldonado
AM, Castillejo MA. Plant proteome analysis: a 2006 update. Proteomics 2007; 7: 2947 …

Development of statistical methods for assessing the significance of peptide assignments to
tandem mass spectra obtained using database searching remains an important problem. In …

Nonalcoholic fatty liver disease (NAFLD), ranging from relatively benign simple steatosis to
progressive nonalcoholic steatohepatitis (NASH) and fibrosis, is an increasingly common …

Major technological advances have made proteomics an extremely active field for biomarker
discovery and validation in recent years. These improvements have lead to an increased …