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In Print: Recent Proteomics Papers of Note: Feb 22, 2013

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In Print: Recent Proteomics Papers of Note

Journal: Proteomics, Jan. 9 [Epub ahead of print]

Title: Extending the coverage of spectral libraries: A neighbor-based approach to predicting intensities of peptide fragmentation spectra.

Authors: Ji C; Arnold RJ; Sokoloski KJ; Hardy RW; Tang H; Radivojac P.

The researchers developed a neighbor-based approach to predict fragment ion intensities corresponding to a given peptide based on the observation that intensity patterns of dominant fragment ions between similar peptides tend to be similar. They predict that the technique could increase the coverage of spectral libraries available from the National Institute of Standards and Technology by 20 percent to 60 percent.


Journal: Scientific Reports, Jan. 9 [Epub ahead of print]

Title: Immune profiling with a Salmonella typhi antigen microarray identifies new diagnostic biomarkers of human typhoid.

Authors: Liang L; Juarez S; Nga TV; Dunstan S; Nakajima-Sasaki R; Davies DH; McSorley S; Baker S; Felgner PL

The researchers used a protein microarray containing 2,724 Salmonella typhi proteins to identify antigens differentially reactive in acute typhoid patients and health controls. They identified antibodies against 16 IgG antigens and 77 IgM antigens, the former distinguishing between patient sets with sensitivity of 97 percent and specificity of 80 percent and the latter with sensitivity of 97 percent and specificity of 91 percent.


Journal: Journal of Proteome Research, Jan. 11 [Epub ahead of print]

Title: Identification of missing proteins in the neXtProt database and unregistered phosphopeptides in the PhosphoSitePlus database as part of the Chromosome-Centric Human Proteome Project.

Authors: Shiromizu T; Adachi J; Watanabe S; Murakami T; Kuga T; Muraoka S; Tomonaga T.

The researchers integrated proteomic and phosphoproteomic data from a number of chromosome-independent biomarker discovery projects to create a chromosome-based list of proteins and phosphorylation sites, identifying 3,033 proteins and 12,852 phosphorylation sites not currently registered in the cited databases.


Journal: Meat Science, Jan. 12 [Epub ahead of print]

Title: Identification of proteomic biomarkers in M. longissimus dorsi as potential predictors of pork quality.

Authors: Te Pas MF; Kruijt L; Pierzchala M; Crump RE; Boeren S; Keuning E; Hoving-Bolink R; Hortós M; Gispert M; Arnau J; Diestre A; Mulder HA.

The authors used NanoLC-FT mass spec to perform proteome profiles of longissimus muscle in pigs, identifying differentially expressed proteins related to drip loss and ultimate pH that could be useful as markers of meat quality.


Journal: Analytical and Bioanalytical Chemistry, Jan. 17 [Epub ahead of print]

Title: Improved detection specificity for plasma proteins by targeting cysteine-containing peptides with photo-SRM.

Authors: Enjalbert Q; Girod M; Simon R; Jeudy J; Chirot F; Salvador A; Antoine R; Dugourd P; Lemoine J.

The authors used photo-SRM for detection of cysteine-containing peptides, finding that compared to standard SRM, photo-SRM, which uses laser-induced photo-dissociation in the visible region at 473 nm, improved detection specificity for most peptides and provided extended response linearity.


Journal: Journal of Proteome Research, Jan. 18 [Epub ahead of print]

Title: Proteome-wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.

Authors: Hahne H; Sobotzki N; Nyberg T; Helm D; Borodkin VS; van Aalten DM; Agnew B; Kuster B.

The authors demonstrate an O-GlcNAc enrichment procedure using metabolic labeling of cells by azide-modified GlcNAc for click chemistry-based purification. Using the technique they identified roughly 1,500 O-GlcNAc proteins. They also used the technique to study the effects of the O-GlcNAcase inhibitor GlcNAcstatin G on the level of O-GlcNAc modification of cellular proteins, identifying 200 proteins that exhibited a change in O-GlcNAc modification in response to the inhibitor.


Journal: Nature Communications, Jan. 29

Title: Deep proteome profiling of Trichoplax adhaerens reveals remarkable features at the origin of metazoan multicellularity.

Authors: Ringrose JH; van den Toorn HW; Eitel M; Post H; Neerincx P; Schierwater B; Maarten Altelaar AF; Heck AJ.

The researchers used high-resolution mass spec to semi-quantify 6,516 proteins in Trichoplax adhaerens, the simplest known animal. According to the abstract, the dataset offers insight into mechanisms underlying the emergence of metazoan multicellularity and is intended as a resource for future research.


Journal: Cell Reports, Jan. 30 [Epub ahead of print]

Title: In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis.

Authors: Zanivan S; Meves A; Behrendt K; Schoof EM; Neilson LJ; Cox J; Tang HR; Kalna G; van Ree JH; van Deursen JM; Trempus CS; Machesky LM; Linding R; Wickström SA; Fässler R; Mann M.

The authors used SILAC-labeled mice combined with high-resolution mass spectrometry to identify phosphoproteomic signatures that distinguish between different skin cancer stages, identifying cell adhesion as a major driver of malignancy and finding the Pak4-PKC/SRC network to be highly deregulated in SCC but not papilloma.


Journal: The Analyst, Jan. 31 [Epub ahead of print]

Title: Realization of on-tissue protein identification by highly efficient in situ digestion with graphene-immobilized trypsin for MALDI imaging analysis.

Authors: Jiao J; Miao A; Zhang X; Cai Y; Lu Y; Zhang Y; Lu H.

The authors presented an implementation of in situ protein digestion using a graphene oxide-immobilized enzyme reactor to simultaneously identify and obtain distribution information of proteins as part of a MALDI imaging mass spec workflow.

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