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A mouse plasma peptide atlas as a resource for disease proteomics
(2008)Genome BiologyWe present an in-depth analysis of mouse plasma leading to the development of a publicly available repository composed of 568 liquid chromatography-tandem mass spectrometry runs. A total of 13,779 distinct peptides have been identified with high confidence. The corresponding approximately 3,000 proteins are estimated to span a 7 logarithmic range of abundance in plasma. A major finding from this study is the identification of novel isoforms ...Journal Article -
Identification of CDK2 substrates in human cell lysates
(2008)Genome BiologyBackground Protein phosphorylation regulates a multitude of biological processes. However, the large number of protein kinases and their substrates generates an enormously complex phosphoproteome. The cyclin-dependent kinases - the CDKs - comprise a class of enzymes that regulate cell cycle progression and play important roles in tumorigenesis. However, despite intense study, only a limited number of mammalian CDK substrates are known. ...Journal Article -
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics
(2008)BMC BioinformaticsBackground Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools is now available for both isotopically labeled and label-free liquid chromatography mass spectrometry (LC-MS) based quantitative proteomics. However, they are generally not comparable to each other in terms of functionality, ...Journal Article -
Selected reaction monitoring for quantitative proteomics: a tutorial
(2008)Molecular Systems BiologySystems biology relies on data sets in which the same group of proteins is consistently identified and precisely quantified across multiple samples, a requirement that is only partially achieved by current proteomics approaches. Selected reaction monitoring (SRM)—also called multiple reaction monitoring—is emerging as a technology that ideally complements the discovery capabilities of shotgun strategies by its unique potential for reliable ...Journal Article -
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The protein information and property explorer: An easy-to-use, rich-client web application for the management and functional analysis of proteomic data
(2008)BioinformaticsJournal Article