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Recent Research Papers of Note in Proteomics: Oct 16, 2008

Journal: Bioinformatics, Oct. 7 [Epub ahead of print]
Title: iPEP: An in silico tool to examine proteolytic peptides for mass spectrometry
Authors: D Lu; RZ Liu; V Izumi; D Fenstermacher; EB Haura; J Koomen; SA Eschrich
Described is a web-based application, iPEP, for comparing different proteolytic digests in the detection of specific sequences. Peptide populations can also be examined to “help optimize detection of certain groups of proteins relative to the proteome and the digested proteome,” according to the abstract. iPEP can help in experimental designing by maximizing the detection of proteins, consensus sites, and modified residues of interest for individual proteins or as part of large-scale proteomic assays, the authors said.

Journal: Journal of Proteome Research, Oct. 7 [Epub ahead of print]
Title: A combination of immobilized pH gradients improves membrane proteomics
Authors: JM Chick; PA Haynes; B Bjellqvist; MS Baker
Authors assess the utility of both broad-range and narrow-range IPG strips for rat liver membrane protein analyses. The use of the strips was evaluated using label-free quantitation to demonstrate the use of narrow-range IPG strips to improve the identification of a subset of proteins.

Journal: Journal of the Royal Society, Interface / the Royal Society, Oct. 6
Title: Spatially selective sampling of single cells using optically trapped fusogenic emulsion droplets: a new single-cell proteomic tool
Authors: PM Lanigan; K Chan; T Ninkovic; RH Templer; PM French; AJ de Mello; KR Willison; PJ Parker; MA Neil; O Ces; DR Klug
A new platform for the spatially selective sampling of the plasma membrane of single cells is presented. Optically trapped lipid-coated oil droplets are brought into contact with target colon cancer cells, forming connecting membrane tethers. Material transfer from the cell to smart droplet microtools across the membrane tether was monitored by tracking membrane-localized enhanced green fluorescent protein.

Journal: Molecular & Cellular Proteomics, Oct. 6 [Epub ahead of print]
Title: BiPS, a photo-cleavable, isotropically-coded, fluorescent crosslinker for structural proteomics
Authors: EV Petrotchenko; K Xiao; J Cable; Y Chen; NV Dokholyan; CH Borchers
The authors say that despite the emergence of crosslinking combined with mass spectrometry as an approach for studying protein structure and protein-protein interactions, unambiguous mass spectrometric identification of crosslinked peptides derived from proteolytically-digested crosslinked proteins remains a challenge. They describe a novel crosslinker, bimane bis-thiopropionic acid n-succinimidyl ester, that overcomes challenges associated with other crosslinking reagents. They said that a “unique” combination of properties distinguishes BiPS from other crosslinkers such as its photo-cleavabiltiy, fluorescence, homo-bifunctionality, amine-reactivity, and isotopic coding.

Journal: Journal of Proteome Research, Oct. 3
Title: Three-layer sandwich gel electrophoresis: A method of salt removal and protein concentration in proteome analysis
Authors: T Liu; AM Martin; AP Sinai; BC Lynn
According to the authors, features of electrospray mass spectrometry “impose limits on the types of buffers, detergents, and reagents that can be used in sample preparation,” though these incompatible reagents significantly enhance protein recoveries from complex mixtures. They suggest that the three-layer sandwich gel electrophoresis protocol can be a better cleanup protocol and provide near quantitative recovery of extremely low concentration proteins from harsh solutions.

Journal: Clinical Cancer Research : An Official Journal of the American Association for Cancer Research, Oct. 1, Oct. 1
Title: Salivary proteomics for oral cancer biomarker discovery
Authors: S Hu; M Arellano; P Boontheung; J Wang; H Zhou; J Jiang; D Elashoff; R Wei; JA Loo; DT Wong
In order to detect the presence of protein biomarkers in human saliva and evaluate their potential as biomarkers for oral squamous cell carcinoma, authors collected saliva samples from 64 patients with OSCC and 64 without. Proteins were profiled using shotgun proteomics, and results were validated with immunoassays. They found five candidate biomarkers which yielded a receiver operating characteristic value of 93 percent, a sensitivity of 90 percent and specificity of 83 percent in detecting OSCC.

Journal: Nature Methods, October
Title: Building consensus spectral libraries for peptide identification in proteomics
Authors: H Lam; DW Deutsch; JS Eddes; JK Eng; SE Stein; R Aebersold
An open-source software toolkit, SpectraST, has been developed to enable researchers to build spectral libraries and to integrate the approach into their data analysis pipeline. SpectraST allows researchers to condense raw data into spectral libraries and to summarize information about observed proteomes into a concise and retrievable format.

Journal: Applied Immunohistochemistry & Molecular Morphology: AIMM / Official Publication of the Society for Applied Immunohistochemistry, October
Title: Evaluation of monospecific antibodies: a comparison study with commercial analogs using immunohistochemistry on tissue microarrays
Authors: L Paavilainen; H Wernérus; P Nilsson; M Uhlén; S Hober; K Wester; F Pontén
Authors said that the generation of monospecific antibodies through affinity purification of polyclonal antisera is a “plausible strategy for high-throughput production of affinity reagents toward large sets of proteins.” In the study they compare 48 msAbs with corresponding commercial analogs. Immunohistochemical staining properties were evaluated on tissue microarrays, representing various normal human tissues from 144 different individuals. They report that msAbs show similar immunostaining patterns as corresponding commercial analogs in 44 out of 48 antibody pairs analyzed. Few antibody pairs showed major discrepancies though minor dissimilarities were frequently seen. “Our results suggest that msAbs are reliable and valuable tools in antibody-based proteomics,” they said in the abstract.

Journal: Rapid Communications in Mass Spectrometry: RCM, October
Title: GlycoMiner: a new software tool to elucidate glycopeptide composition
Authors: O Ozohanics; J Krenyacz; K Ludányi; F Pollreisz; K Vékey; L Drahos
The software, GlycoMiner, automatically identifies MS/MS spectra obtained in LC-MS runs which correspond to N-glycopeptides. The program was tested on tryptic digests of two glycopeptides, AGP and transferrin. Out of 3,132 MS/MS spectra, 338 were found to correspond to glycopeptides. GlycoMiner had a 0.1 percent false-positive rate in identification and 0.1 percent false-negative rate.

Journal: Bioinformatics, Sept. 30 [Epub ahead of print]
Title: MSX-3D: A tool to validate 3D protein models using mass spectrometry
Authors: M Heymann; D Paramelle; G Subra; E Forest; J Martinez; C Geourjon; G Deléage
MSX-3D, a software tool specifically directed at validating protein models using mass spectrometry is introduced. In addition to classic peptide identifications, it allows for the interactive 3D visualization of the distance constraints derived from an experiment using chemical cross-linking.

Journal: Molecular & Cellular Proteomics, Sept. 29 [Epub ahead of print]
Title: SCX-based fractionation of Lys-N generated peptides facilitates the targeted analysis of post-translational modifications
Authors: N Taouatas; AF Altelaar; MM Drugan; AO Helbig; S Mohammed; AJ Heck
Described is a fractionation technique based on the sequential use of strong cation exchange and reversed-phase chromatography to separate peptides generated by a “relatively little explored metalloendopeptidase with a Lys-N cleavage specificity,” according to the abstract. When such proteolytic peptides are subjected to low-pH strong cation exchange, the authors obtained fractionation profiles in which peptides from different functional categories were well separated.

Journal: Applied Microbiology and Biotechnology, Sept. 26 [Epub ahead of print]
Title: Application of sandwich ELISA for detecting tag fusion proteins in high throughput
Authors: ZQ Xu; T Zhang; CJ Song; Q Li; R Zhuang; K Yang; AG Yang; BQ Jin
Authors have developed an ELISA based on monoclonal antibodies against human Ig Fc fragment; GST; maltose-binding protein; and thioredoxin to detect these tag fusion proteins. As a supplement to Western blot, the ELISA was specific, sensitive, quantitative, easy to use, time-saving, and suitable for high-throughput screening of tag fusion proteins, according to the authors.

Journal: Proteomics: Sept. 22 [Epub ahead of print]
Title: A novel method for isolation of membrane proteins: A baculovirus surface display system
Authors: Y Zhang; Z Lu; J Chen; Q Chen; Y Quan; L Kong; H Zhang; S Li; Q Zheng; J Chen; Z Nie; J Want; Y Jin; X Wu
A novel baculovirus surface display system for isolating membrane proteins is reported. Authors expressed a “reporter gene that encoded hemagglutinin gene fused in frame with the signal peptide and transmembrane domaine in the baculovirus gp64 protein, which is displayed on the surface of BmNPV virions,” according to the abstract. As a result of the expression of the fusion protein on the virion envelope, authors developed two methods for isolating membrane proteins. In the first, they isolated proteins directly from the envelope of budding BmNPV virions. In the second, they isolated proteins from cellular membranes that had disintegrated due to viral egress.

Journal: Proteomics, Sept. 22 [Epub ahead of print]
Title: Peptide enrichment and protein fractionation using selective electrophoresis
Authors: L Ly; VC Wasinger
Described is a novel electrophoretic device, MF10, for the fractionation of proteins and peptides based on size and pH in low volume liquid phase under an electric field. A 1microMolar seven protein-and peptide standard mix ranging from 1 to 25 kDa was used to show peptide migration into a fraction contained by 1-5 kDa membranes. Simultaneous fractionation of the higher mass protein standards to the correct fraction also occurred.

Journal: Journal of Proteome Research, Sept. 19 [Epub ahead of print]
Title: A spectral clustering approach to MS/MS identification of post-translational modifications
Authors: JA Falkner; JW Falkner; AK Yocum; PC Andrews
A novel algorithm, Bonanza, for clustering spectra without knowledge of peptide or protein identifications is described. Additional analysis “leverages existing peptide identifications to infer related, likely valid identifications,” the authors said in the abstract. “Significantly” more spectra can be identified using the approach, including those with unexpected potential modifications or amino-acid substitutions.

Journal: BMC Medical Genomics, Sept. 15
Title: A high confidence, manually validated human blood plasma protein reference set
Authors: S Schenk; GJ Schoenhals; G de Souza; M Mann
In order to exploit the “immense diagnostic potential of human plasma,” an “ultra-high” confidence reference list of proteins is necessary, the authors say in the abstract. To address this, they used a linear ion trap Fourier transform and a linear ion trap Orbitrap for mass spectrometry analysis of the human plasma proteome.
They also employed a statistical score that allows database peptide identification searching using the products of two consecutive stages of tandem mass spectrometry. This combined with very high mass accuracy in the parent peptide allows peptide identification with orders of magnitude more confidence than can be typically achieved, the authors said. They identified a set of 697 blood plasma proteins with high confidence with an average sequence coverage of more than 14 peptides per protein and a median of 6 peptides per protein.

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