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SUMMARY The accurate mass and time (AMT) tag approach is used for analysis of large scale experiments by combining information generated over multiple datasets and instrument types. The VIPER software package is one of the key components of the data processing pipeline and implements automated algorithms to discover LC-MS features, align and match these(More)
We report on the design and application of a high-efficiency multiple-capillary liquid chromatography (LC) system for high-throughput proteome analysis. The multiple-capillary LC system using commercial LC pumps was operated at a pressure of 10,000 psi to deliver mobile phases through a novel passive feedback valve arrangement that permitted mobile-phase(More)
BACKGROUND Cancer invasion and metastasis are closely associated with activities within the degradome; however, little is known about whether these activities can be detected in the blood of cancer patients. METHODOLOGY AND PRINCIPAL FINDINGS The peptidome-degradome profiles of pooled blood plasma sampled from 15 breast cancer patients (BCP) and age,(More)
The characterization of cellular proteomes is important for understanding biochemical processes ranging from cell differentiation to cancer development. In one highly promising approach, whole protein extracts or fractions are digested (e.g., with trypsin) and injected into a packed capillary column for subsequent separation. The separated peptides are then(More)
Advanced proteomic research efforts involving areas such as systems biology or biomarker discovery are enabled by the use of high level informatics tools that allow the effective analysis of large quantities of differing types of data originating from various studies. Performing such analyses on a large scale is not feasible without a computational platform(More)
Herein we describe a strategy for degradomic-peptidomic analyses. The human blood peptidome was isolated through application of AC/SEC, which enriched its components by >300-fold. The isolated peptidome components were separated by long column HRLC providing a peak capacity of approximately 300 for species having MWs of up to 20 kDa. The separated species(More)
Complete and accurate genome annotation is crucial for comprehensive and systematic studies of biological systems. However, determining protein-coding genes for most new genomes is almost completely performed by inference using computational predictions with significant documented error rates (> 15%). Furthermore, gene prediction programs provide no(More)
Post-translational modifications (PTMs) of core histones work synergistically to fine tune chromatin structure and function, generating a so-called histone code that can be interpreted by a variety of chromatin interacting proteins. We report a novel online two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS) platform for(More)
Ultrasensitive nanoscale proteomics approaches for characterizing proteins from complex proteomic samples of <50 ng of total mass are described. Protein identifications from 0.5 pg of whole proteome extracts were enabled by ultrahigh sensitivity (<75 zmol for individual proteins) achieved using high-efficiency (peak capacities of approximately 10(3))(More)