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In Print: Recent Proteomics Papers of Note: Nov 15, 2013

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In Print: Recent Proteomics Papers of Note

Journal: Molecular & Cellular Proteomics, Sept. 16 [Epub ahead of print]

Title: Neutron-encoded signatures enable automated product ion annotation from tandem mass spectra.

Authors: Richards AL, Vincent CE, Guthals A, Rose CM, Westphall MS, Bandeira N, Coon JJ.

The authors used neutron-encoded stable isotope labeling of amino acids in cell culture for annotation of C-terminal product ions. Labeling yeast with this method, the researchers observed a 34 percent increase in correct de novo identifications compared to searching with MS/MS alone.


Journal: Analytical Chemistry, Sept 19 [Epub ahead of print]

Title: Long-gradient separations coupled with selected reaction monitoring for highly sensitive, large scale targeted protein quantification in a single analysis.

Authors: Shi T, Fillmore TL, Gao Y, Zhao R, He J, Schepmoes AA, Nicora CD, Wu C, Chambers JL, Moore RJ, Kagan J, Srivastava S, Liu AY, Rodland KD, Liu T, Camp DG 2nd, Smith RD, Qian WJ.

The authors present a method coupling long-gradient separations with selected-reaction monitoring mass spec, finding that moving from a 45 minute gradient to a five hour gradient provided an eight-fold to 100-fold improvement in limits of quantitation for proteins in human female serum. They also demonstrated detection of seven out of eight endogenous plasma proteins expressed at ng/mL or sub-ng/mL levels in clinical patient sera.


Journal: Journal of Proteome Research, Sept. 27 [Epub ahead of print]

Title: The characterization, design, and function of the mitochondrial proteome: From organs to organisms.

Authors: Lotz C, Lin AJ, Black CM, Zhang J, Lau E, Deng N, Wang Y, Zong NC, Choi JH, Xu T, Liem DA, Korge P, Weiss JN, Hermjakob H, Yates JR, Apweiler R, Ping P.

The authors collected data on mitochondrial function and proteomic features from four model systems allowing them to capture the core functionalities of these mitochondria and connect proteomic features with mitochondrial function.


Journal: Journal of Proteome Research, Sept. 27 [Epub ahead of print]

Title: Identification of GABAC receptor protein homeostasis network components from three tandem mass spectrometry proteomics approaches.

Authors: Wang YJ, Han DY, Tabib T, Yates JR, Mu TW.

The authors used three tandem mass spec workflows – gel-based tandem MS (GeLC-MS/MS), solution-based tandem MS (SoLC-MS/MS), and multidimensional protein identification technology – to study the network components of GABAC receptor protein homeostasis, identifying 107 proteins and assembling them within the network.


Journal: Journal of Alzheimer's Disease, Oct. 11 [Epub ahead of print]

Title: Candidate blood proteome markers of Alzheimer's disease onset and progression: A systematic review and replication study.

Authors: Kiddle SJ, Sattlecker M, Proitsi P, Simmons A, Westman E, Bazenet C, Nelson SK, Williams S, Hodges A, Johnston C, Soininen H, Kłoszewska I, Mecocci P, Tsolaki M, Vellas B, Newhouse S, Lovestone S, Dobson R.

The researchers reviewed 21 discovery proteomics studies that had identified blood-based biomarkers for Alzheimer's disease, collecting a total of 163 candidate markers. They then conducted a replication study of 94 of these markers in 677 subjects using SomaLogic's SOMAscan technology, finding that nine of the 94 reporter candidates associated with Alzheimer's.


Journal: Nature Communications, Oct. 18, 2013

Title: Reconstructing targetable pathways in lung cancer by integrating diverse omics data.

Authors: Balbin OA, Prensner JR, Sahu A, Yocum A, Shankar S, Malik R, Fermin D, Dhanasekaran SM, Chandler B, Thomas D, Beer DG, Cao X, Nesvizhskii AI, Chinnaiyan AM.

The authors profiled the transcriptome, proteome, and phosphoproteome of a panle of non-small cell lung cancer cell lines to reconstruct targetable networks associated with KRAS dependency and developed a two-step bioinformatics strategy for integrating these datasets. Using this methodology, they identified LCK as key to cell proliferation in KRAS-dependent but not KRAS-independent NSCLC, suggesting that it is a druggable target in KRAS-dependent disease.


Journal: Journal of Proteomics, Oct. 20 [Epub ahead of print]

Title: Serological autoantibody profiling of type 1 diabetes by protein arrays.

Authors: Miersch S, Bian X, Wallstrom G, Sibani S, Logvinenko T, Wasserfall CH, Schatz D, Atkinson M, Qiu J, Labaer J.

The authors used nucleic acid programmable protein arrays to compare immunoreactivity between type 1 diabetes cases and healthy controls, identifying 26 autoantigens differing between the two sets, including a known TD1-associated autoantigen.


Journal: Journal of Proteome Research, Oct. 28 [Epub ahead of print]

Title: Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies.

Authors: Skates SJ, Gillette MA, Labaer J, Carr SA, Anderson L, Liebler DC, Ransohoff D, Rifai N, Kondratovich M, Težak Z, Mansfield E, Oberg AL, Wright I, Barnes G, Gail M, Mesri M, Kinsinger CR, Rodriguez H, Boja ES.

The authors present a statistical framework for designing biomarker discovery and verification studies, offering an approach for setting statistical criteria for clinical relevance and for calculating necessary sample sizes.

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