Preparation and Use of an Integrated Microcapillary HPLC Column and ESI Device for Proteomic Analysis.

INTRODUCTIONImplementation of separation techniques in miniaturized formats on-line with high-performance mass spectrometers and the development of miniaturized sprayers as electrospray ionization (ESI) ion sources have reduced the amount of peptide required for complete and routine sequence characterization from several picomoles to a few femtomoles and below. Arguably, much of this gain in sensitivity is due to the combination of concentration-dependent type ionization devices such as ESI and on-line capillary separation devices of very small internal diameter (I.D.

Analysis of Phosphopeptides by {micro}LC-ESI-MS/MS.

INTRODUCTIONWhether using a pressure cell or gel-loader tips, IMAC-purified peptides can be injected into a μLC separation system and analyzed by μLC-ESI-MS/MS. Phosphopeptides behave and elute similarly to nonphosphorylated peptides during RP-HPLC, but because of a decrease in hydrophobicity due to the addition of the phosphate moiety, a phosphopeptide will generally elute before the nonphosphopeptide with the identical amino acid sequence. This difference in elution time is most pronounced for short peptides.

Offline Micro-IMAC Enrichment of Phosphoproteins.

INTRODUCTIONImmobilized metal affinity chromatography (IMAC) can be performed offline or online with μLC-ESI-MS/MS. The online configuration has been used successfully despite suboptimal low-level analysis due to the relative disparity between IMAC and μLC flow rates. With IMAC performed offline from μLC-ESI-MS, sample volumes from 1 to 100 μL can be loaded using a sample pressure vessel or an autosampling system equipped with a sample-trapping cartridge.

Characterization of hepatic glutathione S-transferases in coho salmon (Oncorhynchus kisutch).

The glutathione S-transferases (GSTs) are a family of phase II detoxification enzymes which protect against chemical injury. In contrast to mammals, GST expression in fish has not been extensively characterized, especially in the context of detoxifying waterborne pollutants. In the Northwestern United States, coho salmon (Oncorhynchus kisutch) are an important species of Pacific salmon with complex life histories that can include exposure to a variety of compounds including GST substrates.

Electron capture in spin-trap capped peptides. An experimental example of ergodic dissociation in peptide cation-radicals.

Electron capture dissociation was studied with tetradecapeptides and pentadecapeptides that were capped at N-termini with a 2-(4'-carboxypyrid-2'-yl)-4-carboxamide group (pepy), e.g., pepy-AEQLLQEEQLLQEL-NH(2), pepy-AQEFGEQGQKALKQL-NH(2), and pepy-AQEGSEQAQKFFKQL-NH(2).

Lack of in vitro and in vivo recognition of Francisella tularensis subspecies lipopolysaccharide by Toll-like receptors.

Francisella tularensis is an intracellular gram-negative bacterium that is highly infectious and potentially lethal. Several subspecies exist of varying pathogenicity. Infection by only a few organisms is sufficient to cause disease depending on the model system.

Mining the acute respiratory distress syndrome proteome: identification of the insulin-like growth factor (IGF)/IGF-binding protein-3 pathway in acute lung injury.

To obtain a more complete protein profile of the airspace milieu in acute respiratory distress syndrome (ARDS) and to identify new mediators, we analyzed bronchoalveolar lavage fluid (BALF) by shotgun proteomics. Using BALF from three patients, we identified a total of 870 different proteins, a nearly 10-fold increase from previous reports. Among the proteins identified were known markers of lung injury, such as surfactant, proteases, and serum proteins.

Comparison of a Salmonella typhimurium proteome defined by shotgun proteomics directly on an LTQ-FT and by proteome pre-fractionation on an LCQ-DUO.

Shotgun proteomics is rapidly becoming one of the most efficient and popular tools to examine protein expression in cells. Numerous laboratories now have a wide array of low- and high-performance mass spectrometry instrumentation necessary to complete proteome-wide projects. Often these laboratories have time and financial constraints that prohibit all projects from being conducted on high-performance state-of-the-art mass spectrometers.

A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS.

Motivation: Comparing two or more complex protein mixtures using liquid chromatography mass spectrometry (LC-MS) requires multiple analysis steps to locate and quantitate natural peptides within a single experiment and to align and normalize findings across multiple experiments.

Results: We describe msInspect, an open-source application comprising algorithms and visualization tools for the analysis of multiple LC-MS experimental measurements. The platform integrates novel algorithms for detecting signatures of natural peptides within a single LC-MS measurement and combines multiple experimental measurements into a peptide array, which may then be mined using analysis tools traditionally applied to genomic array analysis.

Quantitative proteomic profiling of pancreatic cancer juice.

Pancreatic juice is an exceptionally rich source of cancer-specific proteins shed from cancerous ductal cells into the pancreatic juice. Quantitative proteomic analysis of the proteins specific to pancreatic cancer juice has not previously been reported. We used isotope-code affinity tag (ICAT) technology and MS/MS to perform quantitative protein profiling of pancreatic juice from pancreatic cancer patients and normal controls.

Identification of the interactions between cytochrome P450 2E1 and cytochrome b5 by mass spectrometry and site-directed mutagenesis.

The reaction cycles of cytochrome P450s (P450) require input of two electrons. Electrostatic interactions are considered important driving forces in the association of P450s with their redox partners, which in turn facilitates the transfer of the two electrons. In this study, the cross-linking reagent, 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride (EDC), was used to covalently link cytochrome P450 2E1 (CYP2E1) with cytochrome b(5) (b(5)) through the formation of specific amide bonds between complementary charged residue pairs.

Pro-CrossLink. Software tool for protein cross-linking and mass spectrometry.

To facilitate structural analysis of proteins and protein-protein interactions, we developed Pro-CrossLink, a suite of software tools consisting of three programs (Figure 1), DetectShift, IdentifyXLink, and AssignXLink. DetectShift was developed to detect ions of cross-linked peptide pairs in a mixture of 18O-labeled peptides obtained from protein proteolytic digests. The selected candidate ions of cross-linked peptide pairs subsequently undergo tandem mass spectrometric (MS/MS) analysis for sequence determination.

Proteomic biomarker discovery in cerebrospinal fluid for neurodegenerative diseases.

The clinical diagnosis of major neurodegenerative disorders, e.g. Alzheimer's disease, Parkinson's disease, and dementia with Lewy body, remains unsatisfactory based on current clinical criteria and limited laboratory investigations.

Proteome analysis of Halobacterium sp. NRC-1 facilitated by the biomodule analysis tool BMSorter.

To better understand the extremely halophilic archaeon Halobacterium species NRC-1, we analyzed its soluble proteome by two-dimensional liquid chromatography coupled to electrospray ionization tandem mass spectrometry. A total of 888 unique proteins were identified with a ProteinProphet probability (P) between 0.9 and 1.

Identification of phosphorylation sites using microimmobilized metal affinity chromatography.

One of the most important roles that mass spectrometry (MS) has played in the late twentieth and early twenty-first centuries has been to assist in the growth of knowledge of dynamic phosphorylation events. Not only has MS allowed researches to pinpoint the site of phosphorylation, but it has also enabled them to identify the kinase/phosphatase pairs responsible for regulation of a specific modification as well as to follow the functional consequences of the observed phosphorylation events on the biology of the system. For phosphorylation analysis, the important contribution of MS has been critical but not definitive.

ICAT-based comparative proteomic analysis of non-replicating persistent Mycobacterium tuberculosis.

The non-replicating persistence (NRP) phenotype of Mycobacterium tuberculosis (NRP-TB) is assumed to be responsible for the maintenance of latent infection and the requirement of a long treatment duration for active tuberculosis. Isotope coded affinity tag-based proteomic analysis was used for the determination of the relative expression of large numbers of M. tuberculosis proteins during oxygen self-depletion under controlled conditions in a multi-chambered fermentor.

Stromal mesenchyme cell genes of the human prostate and bladder.

Background: Stromal mesenchyme cells play an important role in epithelial differentiation and likely in cancer as well. Induction of epithelial differentiation is organ-specific, and the genes responsible could be identified through a comparative genomic analysis of the stromal cells from two different organs. These genes might be aberrantly expressed in cancer since cancer could be viewed as due to a defect in stromal signaling.

Improving mass and liquid chromatography based identification of proteins using bayesian scoring.

We present a method for peptide and protein identification based on LC-MS profiling. The method identified peptides at high-throughput without expending the sequencing time necessary for CID spectra based identification. The measurable peptide properties of mass and liquid chromatographic elution conditions are used to characterize and differentiate peptide features, and these peptide features are matched to a reference database from previously acquired and archived LC-MS/MS experiments to generate sequence assignments.

Characterization of microsomal fraction proteome in human lymphoblasts reveals the down-regulation of galectin-1 by interleukin-12.

T helper cells (Th) are divided into Th1 and Th2 subsets based upon their cytokine profiles and function. Naïve Th cells differentiate into Th1 and Th2 subsets depending on the antigens, costimulatory molecules, and cytokines they encounter. Cytokine interleukin (IL)-12 enhances the generation of Th1 lymphocytes and inhibits the production of Th2 subset.

Shotgun proteomic analysis of a chromatophore-enriched preparation from the purple phototrophic bacterium Rhodopseudomonas palustris.

A proteomics approach was evaluated for analysis of photosyntheis-related proteins that are characteristic of chromatophores, particles derived from purple phototrophic bacterial intracytoplasmic membranes. Proteins of purified chromatophores from Rhodopseudomonas palustris were solubilized and digested with trypsin, to create a collection of peptides that were fractionated by liquid chromatography. Peptide sequences were determined and assigned to specific proteins by analysis of tandem mass spectra of peptides, and comparison to a library derived from the recently determined R.

Pancreatic cancer proteome: the proteins that underlie invasion, metastasis, and immunologic escape.

Background & Aims: Pancreatic cancer is a highly lethal disease that has seen little headway in diagnosis and treatment for the past few decades. The effective treatment of pancreatic cancer is critically relying on the diagnosis of the disease at an early stage, which still remains challenging. New experimental approaches, such as quantitative proteomics, have shown great potential for the study of cancer and have opened new opportunities to investigate crucial events underlying pancreatic tumorigenesis and to exploit this knowledge for early detection and better intervention.

Proteomic identification of potential susceptibility factors in drug-induced liver disease.

Drug-induced liver disease (DILD) causes significant morbidity and mortality and impairs new drug development. Currently, no known criteria can predict whether a drug will cause DILD or what risk factors make an individual susceptible. Although it has been shown in mouse studies that the disruption of key regulatory factors, such as cyclooxygenase-2 (COX-2), interleukin (IL)-6, and IL-10, increased susceptibility to DILD caused by acetaminophen (APAP), no single factor seems to be absolute.

Quantitative proteomics of cerebrospinal fluid from patients with Alzheimer disease.

Biomarkers to assist in the diagnosis and medical management of Alzheimer disease (AD) are a pressing need. We have employed a proteomic approach, microcapillary liquid chromatography mass spectrometry of proteins labeled with isotope-coded affinity tags (ICAT), to quantify relative changes in the proteome of human cerebrospinal fluid (CSF) obtained from the lumbar cistern. Using CSF from well-characterized AD patients and age-matched controls at 2 different institutions, we quantified protein concentration ratios of 42% of the 390 CSF proteins that we have identified and found differences > or = 20% in over half of them.