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In Print: Recent Proteomics Papers of Note: May 31, 2013

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In Print: Recent Proteomics Papers of Note

Journal: Hepatology, April 2 [Epub ahead of print]

Title: Imaging mass spectrometry reveals modified forms of histone H4 as new biomarkers of microvascular invasion in hepatocellular carcinomas.

Authors: Poté N; Alexandrov T; Le Faouder J; Laouirem S; Léger T; Mebarki M; Belghiti J; Camadro JM; Bedossa P; Paradis V.

The authors used MALDI imaging mass spec to identify features that would allow them to identify pre-surgery microvascular invasion in hepatocellular carcinoma, identifying modified forms of histone H4 as biomarkers of MiVi.


Journal: Journal of Proteomics, April 2 [Epub ahead of print]

Title: MRI-compatible pipeline for three-dimensional MALDI imaging mass spectrometry using PAXgene fixation.

Authors: Oetjen J; Aichler M; Trede D; Strehlow J; Berger J; Heldmann S; Becker M; Gottschalk M; Kobarg JH; Wirtz S; Schiffler S; Thiele H; Walch A; Maass P; Alexandrov T.

The authors present a new workflow molecular analysis of tissue specimens that integrates 3D MALDI imaging with magnetic resonance imaging, and histological staining and microscopy, applying it to analysis of a mouse kidney. They examined 122 serial sections of a kidney, building a dataset of 2 million MALDI spectra which they integrated with MRI volume rendering and light microscopy data.


Journal: Proceedings of the National Academy of Sciences, April 3 [Epub ahead of print]

Title: Proteome-wide profiling of activated transcription factors with a concatenated tandem array of transcription factor response elements.

Authors: Ding C; Chan DW; Liu W; Liu M; Li D; Song L; Li C; Jin J; Malovannaya A; Jung SY; Zhen B; Wang Y; Qin J.

The authors present an affinity reagent composed of synthetic DNA containing a concatenated tandem array of the consensus transcription factor response elements to a variety of transcription factor families, which enabe broad profiling of transcription factors. Using the reagents, they identified 400 transcription factors from a single cell line and a total of 878 transcription factors from 11 cell types.


Journal: PLoS Computational Biology, April 4 [Epub ahead of print]

Title: Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation.

Authors: Cohen Freue GV; Meredith A; Smith D; Bergman A; Sasaki M; Lam KK; Hollander Z; Opushneva N; Takhar M; Lin D; Wilson-McManus J; Balshaw R; Keown PA; Borchers CH; McManus B; Ng RT; McMaster WR; Biomarkers in Transplantation and the NCE CECR Prevention of Organ Failure Centre of Excellence Teams.

The authors present an end-to-end computational proteomic pipeline for biomarker development, applying it to identifying biomarkers for monitoring acute rejection in cardiac transplantation. Starting with an untargeted screening of the human plasma proteome, they identified five candidate biomarkers, developing MRM-MS assays for these proteins and validating them via ELISA and INA.


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

Title: Glycocapture-assisted global quantitative proteomics (gagQP) reveals multiorgan responses in serum toxicoproteome.

Authors: Sun B; Utleg AG; Hu Z; Qin S; Keller A; Lorang C; Gray L; Brightman A; Lee D; Alexander VM; Ranish JA; Moritz RL; Hood L.

The authors used glycocapture-assisted quantitative proteomics to study serum proteins linked to a mouse model of acetaminophen-induced hepatic and extra-hepatic toxicity, demonstrating the ability of blood-based proteomics to investigate the effects of compound insults impacting multiple organs.


Journal: Molecular & Cellular Proteomics, April 15 [Epub ahead of print]

Title: In silico instrumental response correction improves precision of label-free proteomics and accuracy of proteomics-based predictive models.

Authors: Lyutvinskiy Y; Yang H; Rutishauser D; Zubarev R.

The authors present an in silico post-processing technique for reducing sources of instrument variability in LC-MS/MS workflows, achieving with it coefficients of variation of 1 percent for label-free quantitation of abundant blood plasma proteins.


Journal: Cell Reports, April 18 [Epub ahead of print]

Title: The protein interaction landscape of the human CMGC kinase group.

Authors: Varjosalo M; Keskitalo S; Van Drogen A; Nurkkala H; Vichalkovski A; Aebersold R; Gstaiger M.

The authors performed a global proteomic analysis of the complexes of the human CMGC kinase group, identifying 652 kinase-protein interactions, revealing a kinase-kinase subnetwork and candidate substrates for CMGC kinases.


Journal: Nature Communications, April 23

Title: Identifying sources of tick blood meals using unidentified tandem mass spectral libraries.

Authors: Onder O; Shao W; Kemps BD; Lam H; Brisson D.

The authors used mass spec-based proteomics to identify the source of blood meals of ticks, identifying the vertebrate species from which the blood was derived as much as six months after the tick's feeding.


Journal: PLoS Computational Biology, April 25 [Epub ahead of print]

Title: Distinct types of disorder in the human proteome: functional implications for alternative splicing.

Authors: Colak R; Kim T; Michaut M; Sun M; Irimia M; Bellay J; Myers CL; Blencowe BJ; Kim PM.

Applying two previously developed definitions of intrinsically disordered regions, the authors investigated the presence of "flexible" and "constrained" disordered regions in the human proteome, finding that both types are enriched in regions of proteins that undergo tissue-specific alternative splicing and that flexible disorder is more highly enriched in TS alternative exons while constrained disorder is more highly enriched in exons flanking TS alternative exons. They also showed that cancer driver mutations are enriched in regions of proteins associated with both TS and general AS.

The Scan

And For Adolescents

The US Food and Drug Administration has authorized the Pfizer-BioNTech SARS-CoV-2 vaccine for children between the ages of 12 and 15 years old.

Also of Concern to WHO

The Wall Street Journal reports that the World Health Organization has classified the SARS-CoV-2 variant B.1.617 as a "variant of concern."

Test for Them All

The New York Times reports on the development of combined tests for SARS-CoV-2 and other viruses like influenza.

PNAS Papers on Oral Microbiome Evolution, Snake Toxins, Transcription Factor Binding

In PNAS this week: evolution of oral microbiomes among hominids, comparative genomic analysis of snake toxins, and more.