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In Print: Last Month's Proteomics Papers of Note: May 17, 2012


In Print: Last Month’s Proteomics Papers of Note

Journal: Analytical Chemistry, April 4 [Epub ahead of print]

Title: Carbonyl-reactive tandem mass tags for the proteome-wide quantification of N-linked glycans.

Authors: Hahne H; Neubert P; Kuhn K; Etienne C; Bomgarden R; Rogers JC; Kuster B.

The researchers used stable isotope labeled carbonyl-reactive tandem mass tags for quantification of N-linked glycans. With this approach they characterized the global N-linked glycosylation profiles of two human colon cancer cell lines – SW480 and SW620 – observing down-regulation of high-mannose glycans in the latter.

Journal: Journal of Proteomics, April 4 [Epub ahead of print]

Title: The Silk Road, Marco Polo, a bible and its proteome: A detective story.

Authors: Toniolo L; D'Amato A; Saccenti R; Gulotta D; Righetti PG.

Using mass spec analysis, the researchers identified eight unique cattle proteins from a 700-year-old bible once owned by Khubilai Khan, showing that the book's pages were made from calfskin as opposed to lambskin, as was previously assumed, and demonstrating that proteins can be reliably extracted and identified from ancient parchment.

Journal: Nature Protocols, April 12

Title: Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients.

Authors: Köcher T; Pichler P; Swart R; Mechtler K.

The authors present a protocol for LC-MS/MS analysis of protein from unseparated whole cell extracts, using it to identify 2,761 proteins from a HeLa cell lysate in roughly 10 hours of nanoLC-MS/MS measurement time.

Journal: Proteomics, April 12

Title: Sigpep: Calculating unique peptide signature transition sets in a complete proteome background.

Authors: Helsens K; Mueller M; Hulstaert N; Martens L.

The researchers present a software package called Sigpep for analyzing transition redundancy in SRM-MS assays as well as a web application for generating transition sets for targeted peptides.

Journal: Proteomics, April 18

Title: Why complexity and entropy matter: Information, posttranslational modifications, and assay fidelity.

Authors: Sherman J; Molloy MP; Burlingame AL.

The authors put forth an argument for the use of information theory to define metrics for information and complexity as well as accounting for interference in mass spec-based protein identification.

Journal: PLoS One, April 20 [Epub ahead of print]

Title: Proteomics characterization of cytoplasmic and lipid-associated membrane proteins of human pathogen Mycoplasma fermentans M64.

Authors: Liu YC; Lin IH; Chung WJ; Hu WS; Ng WV; Lu CY; Huang TY; Shu HW; Hsiao KJ; Tsai SF; Chang CH; Lin CH.

The authors used a combination of 2D electrophoresis and Triton X-114 extraction followed by mass spec analysis to identify proteins of pathogenic M. fermentans. Among the identified proteins were a number of M. fermentans that could potentially be used as diagnostic markers or vaccine candidates.

Journal: PLoS One, April 23 [Epub ahead of print]

Title: A proteomic view at T cell costimulation.

Authors: Lichtenfels R; Rappl G; Hombach AA; Recktenwald CV; Dressler SP; Abken H; Seliger B.

The researchers used a 2DE-based proteome analysis of resting T cells versus T cells activated by engagement of the T cell receptor and T cells with activated CD28-mediated signaling in order to investigate changes in the T cell proteome in response to these forms of activation.

Journal: Molecular & Cellular Proteomics, April 24 [Epub ahead of print]

Title: A computational tool to detect and avoid redundancy in selected reaction monitoring.

Authors: Rost HL; Malmstrom L; Aebersold R.

The authors present a computer program, SRMCollider, for calculating non-redundant STM-assays for a given proteomic background to help researchers select peptide optimal peptide transitions for SRM-MS experiments.

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

Title: Systematic comparison of fractionation methods for in-depth analysis of plasma proteomes.

Authors: Cao Z; Tang HY; Wang H; Liu Q; Speicher DW.

The authors compared three different methods – 1D SDS-PAGE, peptide isoelectrofocusing, and peptide high pH reverse-phase chromatography – for fractionating immunodepleted human plasma. They found that high pH reverse-phase chromatography offered the highest peptide resolution and enabled detection of the largest number of known low-abundance proteins.

The Scan

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A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.