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In Print: Recent Proteomics Papers of Note: Oct 4, 2013

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In Print: Recent Proteomics Papers of Note

Journal: Journal of Proteome Research, July 3 [Epub ahead of print]

Title: Label-free selected reaction monitoring enables multiplexed quantitation of S100 protein isoforms in cancer cells.

Authors: Martínez-Aguilar J, Molloy MP.

The authors developed a multiplexed SRM assay to measure the S100 protein isoform family in cancer cells and used it to detect 11 S100 isoforms across a panel of 9 colon and breast cancer cell lines.


Journal: Journal of Proteome Research, July 17 [Epub ahead of print]

Title: Proteogenomic database construction driven from large scale RNA-seq data.

Authors: Woo S, Cha SW, Merrihew G, He Y, Castellana N, Guest C, Maccoss M, Bafna V.

The authors constructed a database containing all useful information expressed in RNA-seq reads in an effort to streamline the integration of RNA-seq and proteomics data. Applying the methods to C elegans data, they reduced 496.2 GB of RNA-seq data to 410 MB, a compression of more than 1000-fold achieved without loss of sensitivity.


Journal: Molecular & Cellular Proteomics, July 22 [Epub ahead of print]

Title: Rapid and deep human proteome analysis by single-dimension shotgun proteomics.

Authors: Pirmoradian M, Budamgunta H, Chingin K, Zhang B, Astorga-Wells J, Zubarev RA.

The authors performed a single-dimension, four-hour LC-MS/MS shotgun proteomics analysis of A375 human cells, identifying 5,354 proteins and 56,390 peptides and achieving roughly 50 percent coverage of the expressed proteome – the highest coverage reported to date for such a workflow, they noted.


Journal: Journal of Proteome Research, July 23 [Epub ahead of print]

Title: Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus Populus.

Authors: Abraham P, Adams RM, Tuskan GA, Hettich RL.

The authors used a peptide sequence tagging approach to analyze sequence variants in the model organism, Populus, detecting 6653 unexpected sequence variants. The also examined how the common chemical modification methionine oxidation could masquerade as a sequence variant.


Journal: Analytical Chemistry, July 24 [Epub ahead of print]

Title: Optimized nonlinear gradients for reversed-phase liquid chromatography in shotgun proteomics.

Authors: Moruz L, Pichler P, Stranzl T, Mechtler K, Käll L.

The authors investigated the use of customized nonlinear gradients for mass spec-based proteomics, developing an algorithm for generating optimized gradient functions. In two experiments each consisting of four replicate runs of a human sample, they found that the optimized gradients produced a more even spread of peptides over the LC run, which led to increased numbers of peptide IDs. The list of peptides identified also differed from those identified using linear gradients, suggesting the approach could be a useful tool for increasing proteome coverage.


Journal: Journal of Proteome Research, Aug. 5 [Epub ahead of print]

Title: Assessment and improvement of statistical tools for comparative proteomics analysis of sparse data sets with few experimental replicates.

Authors: Schwämmle V, León IR, Jensen ON.

The authors assessed the challenges of performing large-scale quantitative proteomic analyses with few replicates and optimized the performance of three statistical approaches – the standard t test, moderated t test, and the rank product method – for the detection of significantly changing analytes in proteomics datasets.


Journal: Nature, Aug. 7 [Epub ahead of print]

Title: Coordination of bacterial proteome with metabolism by cyclic AMP signalling.

Authors: You C, Okano H, Hui S, Zhang Z, Kim M, Gunderson CW, Wang YP, Lenz P, Yan D, Hwa T.

The authors used a quantitative proteomic analysis to demonstrate that cAMP signaling tightly coordinates the expression of catabolic proteins with biosynthetic and ribosomal protein and proposed and validated a scheme of feedback control involving cAMP signaling by metabolic precursors.


Journal: Journal of Proteome Research, Aug. 13 [Epub ahead of print]

Title: Quantitative proteomics profiling of primary lung adenocarcinoma tumors reveals functional perturbations in tumor metabolism.

Authors: Pernemalm M, De Petris L, Branca RM, Forshed J, Kanter L, Soria JC, Girard P, Validire P, Pawitan Y, van den Oord J, Lazar V, Påhlman S, Lewensohn R, Lehtiö J.

The authors used mass spec to analyze human primary lung adenocarcinoma tumors, identifying 132 proteins that separated groups according to relapse rates. Via analysis of these proteins they hypothesized that tumors with poor prognosis had a higher glycolytic activity and HIF activation.


Journal: Journal of Proteome Research, Aug. 16 [Epub ahead of print]

Title: Hyperplex-MRM: A hybrid multiple reaction monitoring method using mTRAQ/iTRAQ labeling for multiplex absolute quantification of human colorectal cancer biomarker.

Authors: Yin HR, Zhang L, Xie LQ, Huang LY, Xu Y, Cai SJ, Yang PY, Lu HJ.

The authors present an MRM-based protein quantitation metghod that combines mTRAQ and iTRAQ labeling to increase throughput and reliability, allowing them to perform absolute quantification of target peptides in four different samples in a single run. Using the approach they quantified three biomarker candidates in colorectal cancer tissue, achieving high accuracy, sensitivity, and reproducibility.

The Scan

WHO Seeks Booster Pause

According to CNN, the World Health Organization is calling for a moratorium on administering SARS-CoV-2 vaccine boosters until more of the world has received initial doses.

For Those Long Legs

With its genome sequence and subsequent RNAi analyses, researchers have examined the genes that give long legs to daddy longlegs, New Scientist says.

September Plans

The New York Times reports that the US Food and Drug Administration is aiming for early September for full approval of the Pfizer-BioNTech SARS-CoV-2 vaccine.

Nucleic Acids Research Papers on Targeting DNA Damage Response, TSMiner, VarSAn

In Nucleic Acids Research this week: genetic changes affecting DNA damage response inhibitor response, "time-series miner" approach, and more.