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In Print: Recent Proteomics Papers of Note: Jul 6, 2012


In Print: Recent Proteomics Papers of Note

Journal: Proceedings of the National Academy of Sciences, May 7, [Epub ahead of print]

Title: Probing isoform-specific functions of polypeptide GalNAc-transferases using zinc finger nuclease glycoengineered SimpleCells.

Authors: Schjoldager KT; Vakhrushev SY; Kong Y; Steentoft C; Nudelman AS; Pedersen NB; Wandall HH; Mandel U; Bennett EP; Levery SB; Clausen H.

The authors extended the use of gycloengineered SimpleCells – human cell lines deficient in O-glycan extension to allow proteome-wide discovery of O-glycoproteins – to include proteome-wide discovery of functions of individual GalNAc-Ts.

Journal: Journal of Proteomics, May 9 [Epub ahead of print]

Title: Immunoassay-based proteome profiling of 24 pancreatic cancer cell lines.

Authors: Alhamdani MS; Youns M; Buchholz M; Gress TM; Beckers MC; Maréchal D; Bauer A; Schröder C; Hoheisel JD.

The authors analyzed the proteomics of 24 pancreatic cell lines and two controls using an antibody array targeting 741 cancer-related proteins, finding 72 potential disease markers not previously identified. They also identified 187 proteins that were differentially expressed in primary versus metastatic cells – most of which were involved in cellular movement.

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

Title: Robust two-dimensional separation of intact proteins for bottom-up tandem mass spectrometry of the human CSF proteome.

Authors: Bora A; Anderson C; Bachani M; Nath A; Cotter RJ.

The authors presented a gel-free sample prep method for mass spec analysis of human cerebrospinal fluid, which they used to enable identification of low abundance CSF proteins in a high-throughput manner.

Journal: PLoS One, May 16 [Epub ahead of print]

Title: Urinary proteomics to support diagnosis of stroke.

Authors: Dawson J; Walters M; Delles C; Mischak H; Mullen W.

The authors used time-of-flight mass spectrometry to identify urinary protein biomarkers that could be used to diagnose ischemic stroke. They developed two panels – one a 14-protein panel and the other a 35-protein panel, the latter of which performed with AUROC of .86.

Journal: Proteomics, May 23 [Epub ahead of print]

Title: Quantitative proteomics of primary tumors with varying metastatic capabilities using stable isotope-labeled proteins of multiple histogenic origins.

Authors: Lund RR; Terp MG; Laenkholm AV; Jensen ON; Leth-Larsen R; Ditzel HJ.

The authors identified proteins involved in the colonization phase of metastasis by comparing the proteomes of tumors derived from introducing a panel of cancer cell lines with different metastatic capabilities into the mammary fat pad of immunodeficient mice. They identified a total of 675 different proteins, 30 of which were differentially expressed between at least two of the tumors.

Journal: Molecular & Cellular Proteomics, May 29 [Epub ahead of print]

Title: Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse.

Authors: Trinidad JC; Barkan DT; Gulledge BF; Thalhammer A; Sali A; Schoepfer R; Burlingame AL.

The authors identified more than 1,750 and 16,500 sites of O-GlcNAcylation and phosphorylation in mouse synaptosomes, respectively, identifying the potential for crosstalk between the two post-translational modifications.

Journal: Molecular & Cellular Proteomics, May 30 [Epub ahead of print]

Title: Identification of new autoantigens for primary biliary cirrhosis using human proteome microarrays.

Authors: Hu CJ; Song G; Huang W; Liu GZ; Deng CW; Zeng HP; Wang L; Zhang FC; Zhang X; Jeong JS; Blackshaw S; Jiang LZ; Zhu H; Wu L; Li YZ.

The authors used a human proteome microarray featuring 17,000 full-length unique proteins to screen for proteins correlated with primary biliary cirrhosis. They then screened these proteins against cohorts of 191 PBC patients and 321 controls, identifying six as novel PBC autoantigens, of which they developed ELISAs for two and tested in larger cohorts to confirm the results.

Journal: Molecular & Cellular Proteomics, June 1 [Epub ahead of print]

Title: Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.

Authors: Hahne H; Gholami AM; Kuster B.

The authors assessed to what extent O-GlcNAc-modified proteins could be identified from existing large-scale proteomic data sets using their recently developed Oscore software to analyze tandem mass spectra for the modification. Reanalyzing several datasets, they extended the number of known O-GlcNAc-modified proteins by more than 100, suggesting that the modification is considerably more abundant than previously thought.

Journal: Frontiers in Plant Science, June 11 [Epub ahead of print]

Title: Pep2pro: the high-throughput proteomics data processing, analysis, and visualization tool.

Authors: Hirsch-Hoffmann M; Gruissem W; Baerenfaller K.

The authors presented a database for high-throughput proteome data analysis that enables the integration of search results from different database-dependent search algorithms.

Journal: Journal of Proteome Research, June 14 [Epub ahead of print]

Title: Automated selected reaction monitoring software for accurate label-free protein quantification.

Authors: Teleman J; Karlsson C; Waldemarson S; Hansson K; James P; Malmström J; Levander F.

The researchers developed a new algorithm, Anubis, for more accurate peak detection in label-free selected-reaction monitoring mass spec workflows. Using it to measure complex peptide mixtures from whole proteome digests of Steptococcus pyogenes, they achieved technical variability of between 6.5 percent and 19.2 percent.

Journal: The EMBO Journal, June 22 [Epub ahead of print]

Title: Secretome protein enrichment identifies physiological BACE1 protease substrates in neurons.

Authors: Kuhn PH; Koroniak K; Hogl S; Colombo A; Zeitschel U; Willem M; Volbracht C; Schepers U; Imhof A; Hoffmeister A; Haass C; Roßner S; Bräse S; Lichtenthaler SF.

The researchers presented a method for proteome-wide identification of shedding substrates and secreted proteins from primary cells called secretome protein enrichment with click sugars, or SPECS. They used the method to identify BACE1 protease substrates in neurons, identifying 34 substrates, most of them novel.

Journal: PLoS One, June 22 [Epub ahead of print]

Title: Partitioning the proteome: phase separation for targeted analysis of membrane proteins in human post-mortem brain.

Authors: English JA; Manadas B; Scaife C; Cotter DR; Dunn MJ.

The researchers developed a workflow to enrich and study membrane proteins in human post-mortem brain tissue using Triton X-114 phase separation and LC-MS/MS analysis. They identified 494 membrane proteins, with 194 trans-membrane helices present, at a rate of between 1 and 21 helices per protein.

Journal: Proceedings of the National Academy of Sciences, June 25, [Epub ahead of print]

Title: Quantitative assessment of the impact of the gut microbiota on lysine {varepsilon}-acetylation of host proteins using gnotobiotic mice.

Authors: Simon GM; Cheng J; Gordon JI.

The researchers examined the affect of gut microbiota on lysine acetylation in mouse proteomes, observing increases in lysine acetylation in germ-free mice upon introduction of microbiota harvested from conventionally raised mice. They found that the acetylated proteins were enriched in functions related to energy production, respiration, and primary metabolism.

Journal: Journal of Proteome Research, June 26 [Epub ahead of print]

Title: GeLC-MRM quantitation of mutant KRAS oncoprotein in complex biological samples.

Authors: Halvey PJ; Ferrone CR; Liebler DC.

The researchers detailed a gel electrophoresis-based strategy for enriching KRAS oncoproteins from cancer cell lines for analysis by multiple-reaction monitoring mass spec.

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.