Ruihua Fang

TL;DR: High-efficiency nanoscale reversed-phase liquid chromatography was used to obtain ultra-high-efficiency separations in conjunction with tandem mass spectrometry (MS/MS) for characterization of the human plasma proteome and enabled the identification of proteins over a dynamic range of greater than 8 orders of magnitude in relative abundance using ion trap MS/MS instrumentation.

TL;DR: msInspect is described, an open-source application comprising algorithms and visualization tools for the analysis of multiple LC-MS experimental measurements and combines multiple experimental measurements into a peptide array, which may then be mined using analysis tools traditionally applied to genomic array analysis.

TL;DR: The open-source Computational Proteomics Analysis System (CPAS) contains an entire data analysis and management pipeline for Liquid Chromatography Tandem Mass Spectrometry proteomics, including experiment annotation, protein database searching and sequence management, and mining LC-MS/MS peptide and protein identifications.

TL;DR: The results of this study provide a basis for a wide range of plasma proteomics studies, including broad quantitation of relative abundances in comparative studies of the identification of novel protein disease markers, as well as further studies of protein‐protein interactions.

TL;DR: A head-to-head comparison of several serum fractionation schemes, including N-linked glycopeptide enrichment, cysteinyl-peptides enrichment, magnetic bead separation, size fractionation, protein A/G depletion, and immunoaffinity column depletion of abundant serum proteins, shows immunoAffinity subtraction is the most effective means for simplifying the serum proteome while maintaining reasonable sample throughput.