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In Print: Recent Proteomics Papers of Note: Jul 8, 2013

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In Print: Recent Proteomics Papers of Note

Journal: Analytical Chemistry, May 6

Title: Large-scale analysis of peptide sequence variants: the case for high-field asymmetric waveform ion mobility spectrometry.

Authors: Creese AJ; Smart J; Cooper HJ.

The authors investigated the benefits of FAIMS for identification and quantification of peptide isomers, using it to analyze a phosphopeptide library containing numerous sequence inversions and structural isomers. Using FAIMS, they identified 35 percent of the library, compared to 8 percent by LC-MS/MS alone and 17 percent by LC-MS/MS with strong cation exchange chromatography.


Journal: Cell Host & Microbe, May 15

Title: The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis.

Authors: Schubert OT; Mouritsen J; Ludwig C; Röst HL; Rosenberger G; Arthur PK; Claassen M; Campbell DS; Sun Z; Farrah T; Gengenbacher M; Maiolica A; Kaufmann SH; Moritz RL; Aebersold R.

The authors present a series of selected-reaction monitoring mass spec assays for quantifying 97 percent of the 4,012 annotated Mtb proteins, using it to monitor the Mtb dormancy survival regulon and its dynamic protein-level regulation during hypoxia.


Journal: PLoS One, May 20

Title: Quantitative label-free proteomics for discovery of biomarkers in cerebrospinal fluid: assessment of technical and inter-individual variation.

Authors: Perrin RJ; Payton JE; Malone JP; Gilmore P; Davis AE; Xiong C; Fagan AM; Townsend RR; Holtzman DM.

The authors examined the technical and inter-individual variation of label-free quantitative shotgun proteomics, finding that the technique can measure CSF protein levels with low technical variability, making it potential suitable for biomarker discovery.


Journal: Molecular & Cellular Proteomics, May 21 [Epub ahead of print]

Title: High-throughput database search and large-scale negative polarity LC-MS/MS with ultraviolet photodissociation for complex proteomic samples.

Authors: Madsen JA; Xu H; Robinson MR; Horton AP; Shaw JB; Giles DK; Kaoud TS; Dalby KN; Trent MS; Brodbelt JS.

The authors present a database search algorithm, MassMatrix, to facilitate the interpretation and assignment of mass spectra generated with the use of ultraviolet photodissociation.


Journal: Journal of Proteome Research, May 22 [Epub ahead of print]

Title: Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer.

Authors: Zhang EY; Cristofanilli M; Robertson F; Reuben JM; Mu Z; Beavis RC; Im H; Snyder M; Hofree M; Ideker T; Omenn GS; Fanayan S; Jeong SK; Paik YK; Zhang AF; Wu SL; Hancock WS.

The authors performed an integration of transcriptomic and proteomic data generated from three breast cancer cell lines, using RNA-seq to identifying oncogenes with significant transcripts in these cell lines and proteomics to identify proteins with significant interactions with these oncogenes. In this way they identified four major oncogenes for pathway analysis, through which they identified several potential proteomic signatures.


Journal: Proteomics, May 22 [Epub ahead of print]

Title: A new insight into the impact of different proteases on SILAC quantitative proteome of the mouse liver.

Authors: Ma J; Li W; Lv Y; Chang C; Wu S; Song L; Ding C; Wei H; He F; Jiang Y; Zhu Y.

The authors examined the use of multiple proteases on protein identification and quantification of SILAC-labeled mouse liver finding that trypsin and tandem LysC/trypsin digestion are superior to LysC in peptides and protein identification while LysC shows advantages in quantification of Lys-labeled proteins. The results suggest that combining these approaches could provide improvements in qualitative and quantitative proteomics result, they wrote in the abstract.


Journal: Experimental and Molecular Pathology, May 24 [Epub ahead of print]

Title: Protein from the fraction remaining after RNA extraction is useful for proteomics but care must be exercised in its application.

Authors: Yamaguchi H; Hasegawa K; Esumi M.

The authors investigated the simultaneous extraction of mRNA and protein from biopsy specimens, offering a method for extracting the protein after RNA isolation and finding that while quantitative profiles of individual proteins extracted in this manner were different from conventionally isolated samples, the overall profiles were similar.


Journal: Journal of Proteome Research, May 30 [Epub ahead of print]

Title: Blood plasma reference material: a global resource for proteomic research.

Authors: Malm J; Danmyr P; Nilsson R; Appelqvist R; Végvári A; Marko-Varga G.

The authors present a new set of reference blood plasma standards based on 80 patient samples each from newborn children one to two weeks; subjects aged 15 to 30; 30 to 50; and 65 and older. The samples can be accessed upon request and are intended as a high quality resource for global proteomics research.


Journal: Journal of Proteome Research, May 30 [Epub ahead of print]

Title: Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides.

Authors: Guthals A; Clauser KR; Frank AM; Bandeira N.

The authors combined electron-transfer dissociation with collision-induced dissociation and higher-energy collision-induced dissociation fragmentation to improve interpretation of long, highly charged peptides.

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.