There is an increasing need in biology and clinical medicine to robustly and reliably measure tens to hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility, and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here, we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and seven control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data, we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to subnanogram/ml sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intraand interlaboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy-isotope-labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participatFrom the A Broad Institute of MIT and Harvard,

Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological andclinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers. The SSP was designed for use with low multiplex analyses as well as high multiplex approaches when software-driven scheduling of data acquisition is required. Performance was assessed by monitoring of a range of chromatographic and mass spectrometric metrics including peak width, chromatographic resolution, peak capacity, and the variability in peak area and analyte retention time (RT) stability. The SSP, which was evaluated in 11 laboratories on a total of 15 different instruments, enabled early diagnoses of LC and MS anomalies that indicated suboptimal LC-MRM-MS performance. The observed range in variation of each of the metrics scrutinized serves to define the criteria for optimized LC-SID-MRM-MS platforms for routine use, with pass/fail criteria for system suitability performance measures defined as peak area coefficient of variation <0.15, peak width coefficient of variation <0.15, standard deviation of RT <0.15 min (9 s), and the RT drift <0.5min (30 s). The deleterious effect of a marginally performing LC-SID-MRM-MS system From the ‡Broad Institute of MIT and Harvard,

Microarrays containing up to three different proteins were fabricated by microcontact printing (µCP) techniques and tested as a detection system for specific antibodies. After fabrication, immunoassays were successfully performed using the patterned protein microarrays. The developed immunoassays were characterized by fluorescence microscopy and scanning probe microscopy. The characterization revealed the quality of the protein deposition and indicated a high degree of selectivity for the targeted antigenantibody interactions. The results of this study suggest that µCP is an inexpensive and effective way to fabricate biologically active substrates that can be of use for multiple reagentless immunosensor applications.

A new strategy for specifically targeting cysteine-containing peptides in a tryptic digest is described. The method is based on quantitatively derivatizing cysteine residues with a quaternary amine tag (QAT). Tags were introduced into proteins following reduction of disulfide bonds through derivatization of cysteine residues with (3-acrylamidopropyl)trimethylammonium chloride. After trypsin digestion, derivatized cysteine-containing peptides were enriched by strong cation exchange chromatography. The method was validated using model peptides and a protein. The QAT strategy has several advantages over other methods for the selection of cysteine-containing peptides. One is that it increases the ionization efficiency of cysteine-containing peptides. The other is that chromatographic selection is achieved with simple, robust cation exchange chromatography columns. As a result, this new strategy provides a simple way to facilitate enrichment of cysteine-containing peptides, thereby reducing sample complexity in bottom-up proteomics.

A novel acid-labile poly(ethylene glycol) (PEG)-conjugated lipid, (R)-1,2-di-O-(1′Z,9′Z-octadecadienyl)glyceryl-3-(ω-methoxy-poly(ethylene glycolate, MW5000) (BVEP), a neutral PEG-derivatized analogue of diplasmenylcholine, has been used at low molar ratios to disperse the nonlamellar, fusogenic lipid 1,2dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) as unilamellar liposomes. It was anticipated that acidcatalyzed hydrolysis of the vinyl ether linkages would destabilize BVEP/DOPE liposomes by removal of the water-soluble, sterically stabilizing PEG layer, thereby promoting contents release and membranemembrane fusion. This paper describes the hydrolysis rates, contents release rates, and fusion kinetics of BVEP-stabilized DOPE liposomes at 1:99, 3:97, and 5:95 molar ratios of BVEP/DOPE. Calcein leakage kinetics indicate that 3:97 BVEP/DOPE liposomes offer the best stability at pH 7.4 while retaining favorable leakage properties at pH 4.5 (t50%release ≈ 4 h). N-Rhodamine phosphatidylethanolamine/N-nitrobenzoxadiazole phosphatidylethanolamine lipid mixing assays show that membrane fusion occurs on a much slower time scale than leakage in these systems, with ∼12% lipid mixing occurring over a 24 h time period at pH 2.0. No appreciable membrane fusion occurred in these liposomes at either pH 7.4 or 4.5 when monitored for up to 3 days. 31 P NMR spectra at pH 7.4 contain a single isotropic line shape, consistent with the presence of large liposomes. The 31 P NMR line shape did not change significantly even after long exposure times at pH 4.0; however, Mn 2+ addition experiments with acid-treated samples produced linebroadened spectra, indicating that all the phosphorus sites were continuous with the bulk water phase. Time-dependent cryogenic transmission electron microscopy experiments indicate that extensive liposome collapse to give small dense aggregates occurs over a 1-4 h period when 3:97 BVEP/DOPE liposomes are acidified to pH 4.5. Taken together, these results suggest that acid-catalyzed hydrolysis of BVEP/DOPE liposomes does result in dePEGylative triggering; however, the primary outcome of this cleavage process is contents leakage and liposome collapse to give <100 nm particles that are presumed to be inverted hexagonal phase structures, with membrane lipid mixing occurring on a kinetically slower time scale. † Dedicated to the memory of David F. O'Brien, deceased July 2002.

BackgroundTicks (Family Ixodidae) transmit a variety of disease causing agents to humans and animals. The tick-borne flaviviruses (TBFs; family Flaviviridae) are a complex of viruses, many of which cause encephalitis and hemorrhagic fever, and represent global threats to human health and biosecurity. Pathogenesis has been well studied in human and animal disease models. Equivalent analyses of tick-flavivirus interactions are limited and represent an area of study that could reveal novel approaches for TBF control.Methodology/Principal FindingsHigh resolution LC-MS/MS was used to analyze the proteome of Ixodes scapularis (Lyme disease tick) embryonic ISE6 cells following infection with Langat virus (LGTV) and identify proteins associated with viral infection and replication. Maximal LGTV infection of cells and determination of peak release of infectious virus, was observed at 36 hours post infection (hpi). Proteins were extracted from ISE6 cells treated with LGTV and non-infectious (UV inactivated) LGTV at 36 hpi and analyzed by mass spectrometry. The Omics Discovery Pipeline (ODP) identified thousands of MS peaks. Protein homology searches against the I. scapularis IscaW1 genome assembly identified a total of 486 proteins that were subsequently assigned to putative functional pathways using searches against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. 266 proteins were differentially expressed following LGTV infection relative to non-infected (mock) cells. Of these, 68 proteins exhibited increased expression and 198 proteins had decreased expression. The majority of the former were classified in the KEGG pathways: “translation”, “amino acid metabolism”, and “protein folding/sorting/degradation”. Finally, Trichostatin A and Oligomycin A increased and decreased LGTV replication in vitro in ISE6 cells, respectively.Conclusions/SignificanceProteomic analyses revealed ISE6 proteins that were differentially expressed at the peak of LGTV replication. Proteins with increased expression following infection were associated with cellular metabolic pathways and glutaminolysis. In vitro assays using small molecules implicate malate dehydrogenase (MDH2), the citrate cycle, cellular acetylation, and electron transport chain processes in viral replication. Proteins were identified that may be required for TBF infection of ISE6 cells. These proteins are candidates for functional studies and targets for the development of transmission-blocking vaccines and drugs.

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An acid-cleavable PEG lipid, 1′-(4′-cholesteryloxy-3′-butenyl)-ω-methoxy-polyethylene [112] glycolate (CVEP), has been developed that produces stable liposomes when dispersed as a minor component (0.5-5 mol%) in 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE). Cleavage of CVEP at mildly acidic pH's results in dePEGylation of the latently fusogenic DOPE liposomes, thereby triggering the onset of contents release. This paper describes the synthesis of CVEP via a six step sequence starting from the readily available precursors 1,4-butanediol, cholesterol, and mPEG acid. The hydrolysis rates and release kinetics from CVEP:DOPE liposome dispersions as a function of CVEP loading, as well as the cryogenic transmission electron microscopy and pH-dependent monolayer properties of 9:91 CVEP:DOPE mixtures, also are reported. When folate-receptor positive KB cells were exposed to calcein-loaded 5:95 CVEP:DOPE liposomes containing 0.1 mol% folatemodified 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-polyethylene[76] glycolamide (folate-PEG-DSPE), efficient delivery of the calcein cargo to the cytoplasm of the cells was observed as determined by fluorescence microscopy and flow cytometry. Fluorescence resonance energy transfer analysis of lipid mixing in these cells was consistent with membrane-membrane fusion between the liposome and endosomal membranes.