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In Print: Recent Proteomics Papers of Note: Jan 17, 2014

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In Print: Recent Proteomics Papers of Note

Journal: Molecular & Cellular Proteomics, Nov. 4 [Epub ahead of print]

Title: N-linked glycosylation enrichment for in-depth cell surface proteomics of diffuse large B-cell lymphoma subtypes.

Authors: Deeb SJ, Cox J, Schmidt-Supprian M, Mann M.

The authors use N-glyco FASP with super-SILAC to quantify N-linked glycoproteins in lymphoma cells, finding that analysis of the N-glyco subproteome alone allowed them to distinguish between ABC and GCB subtypes in lymphoma.


Journal: Journal of Proteome Research, Nov. 19 [Epub ahead of print]

Title: Comparison of protein immunoprecipitation-multiple reaction monitoring with ELISA for assay of biomarker candidates in plasma.

Authors: Lin D, Alborn WE, Slebos RJ, Liebler DC.

The researchers compared immunoprecipitation MRM to ELISA for the analysis of six colon cancer biomarkers finding high levels of correlation between the two methods, suggesting that IP-MRM is an effective alternative to ELISA for protein quantitation.


Journal: PLOS One, Nov. 27

Title: A novel pulse-chase SILAC strategy measures changes in protein decay and synthesis rates induced by perturbation of proteostasis with an Hsp90 inhibitor.

Authors: Fierro-Monti I, Racle J, Hernandez C, Waridel P, Hatzimanikatis V, Quadroni M.

The authors developes a pulse-chase SILAC method capable of simultaneously quantifying for two conditions the relative levels of proteins newly synthesized in a given time along with the levels of preexisting proteins and validated the method by studying the drug-mediated inhibition of Hsp90.


Journal: Nature Methods, Dec. 1 [Epub ahead of print]

Title: A chemoproteomic platform to quantitatively map targets of lipid-derived electrophiles.

Authors: Wang C, Weerapana E, Blewett MM, Cravatt BF.

The researchers present a competitive activity-based profiling system for quantifying the reactivity of electrophilic compounds against more than 1,000 systems in parallel in the human proteome. They used the methods to identify proteins particularly amenable to modification by lipid-derived electrophiles.


Journal: Journal of Proteome Research, Dec. 2 [Epub ahead of print]

Title: Simplified quantitative glycomics using the stable isotope label Girard's reagent P by electrospray ionization mass spectrometry.

Authors: Wang C, Wu Z, Yuan J, Wang B, Zhang P, Zhang Y, Wang Z, Huang L.

The authors used Girard's reagent P to simplify the mass spec profiles of derivatives of neutral glycans to allow more rapid and sensitive quantification and comparison between different glycan samples.


Journal: Journal of Proteome Research, Dec. 6 [Epub ahead of print]

Title: State of the human proteome in 2013 as viewed through PeptideAtlas: Comparing the kidney, urine, and plasma proteomes for the Biology- and Disease-Driven Human Proteome Project.

Authors: Farrah T, Deutsch EW, Omenn GS, Sun Z, Watts JD, Yamamoto T, Shteynberg D, Harris MM, Moritz RL.

The authors presented data from the current edition of PeptideAtlas as a glimpse at the state of the human proteome. According to the authors, the analysis "yielded 4,005, 2,491, and 3,553 nonredundant proteins at 1 percent FDR for the kidney, urine, and plasma proteomes, respectively" and 12,644 non-redundant proteins for the entire human proteome and at least one peptide for roughly 14,000 Swiss-Prot entries.


Journal: Nature Methods, Dec. 8 [Epub ahead of print]

Title: Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins.

Authors:Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG.

The authors present a set of 645 novel MRM mass spec assays to 319 proteins in human breast cancer validated across three laboratories. The assays are multiplexed in groups of 150 or more peptides and have a median precision of 5.4 percent.


Journal: Journal of Proteome Research, Dec. 12 [Epub ahead of print]

Title: Identification of novel biomarkers of brain damage in patients with hemorrhagic stroke by integrating bioinformatics and mass spectrometry-based proteomics.

Authors: Martínez-Morillo E, García Hernández P, Begcevic I, Kosanam H, Prieto García B, Alvarez Menéndez FV, Diamandis EP.

Using the Human Protein Atlas and PeptideAtlas databases, the researchers selected proteins specifically and abundantly expressed in brain tissue to which they developed SRM assays, measuring them in 36 age-matched patients including those with hemorrhagic stroke, ischemic stroke, and controls, identifying biomarkers for brain hemorrhage.


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

Title: Accounting for population variation in targeted proteomics.

Authors: Fujimoto GM, Monroe ME, Rodriguez L, Wu C, Maclean B, Smith RD, Maccoss MJ, Payne SH.

The authors present the Population Variation plug-in for Skyline, a tool for providing access to polymorphisms stored in dbSNP. Given a set of peptides, the tool reports minor allele frequency for common polymorphisms, helping researchers identify target peptides with high variability in humans to assist in accounting for biological variability in targeted proteomics experiments.

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