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In Print: Recent Proteomics Papers of Note: Aug 15, 2014

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In Print: Recent Proteomics Papers of Note

Journal: Journal of Proteome Research, May 14 [Epub ahead of print]

Title: Integrating meta-analysis of microarray data and targeted proteomics for biomarker identification: application in breast cancer.

Authors: Pavlou MP, Dimitromanolakis A, Martinez-Morillo E, Smid M, Foekens JA, Diamandis EP.

The researchers used transcriptomic and proteomic platforms to identify candidate biomarkers for breast cancer, developing a mass spec assay for quantification of 20 proteins. Measuring these 20 proteins in 96 samples from patients with early stage breast cancer they identified two proteins KPNA2 and CDK1 that showed potential for identifying estrogen receptor-positive patients with at high risk of recurrence.


Journal: Nature Communications, May 29

Title: A pan-cancer proteomic perspective on The Cancer Genome Atlas.

Authors: Akbani R, Ng PK, Werner HM, Shahmoradgoli M, Zhang F, Ju Z, Liu W, Yang JY, Yoshihara K, Li J, Ling S, Seviour EG, Ram PT, Minna JD, Diao L, Tong P, Heymach JV, Hill SM, Dondelinger F, Städler N, Byers LA, Meric-Bernstam F, Weinstein JN, Broom BM, Verhaak RG, Liang H, Mukherjee S, Lu Y, Mills GB.

The authors used reverse-phase protein arrays to analyze 3,467 patient samples across 11 cancers from The Cancer Genome Atlas project. Measuring 128 proteins and 53 post-translational modifications, they identified patterns and sub-patterns of expression and pathway activation across and within tumor sets.


Journal: Proteomics, June 11 [Epub ahead of print]

Title: Development and performance evaluation of an ultralow flow nanoliquid chromatography-tandem mass spectrometry set-up.

Authors: Köcher T, Pichler P, De Pra M, Rieux L, Swart R, Mechtler K.

The authors present a nano LC system with a flow rate of 20 nL/min for routine proteomic analysis. Using 100 ng of sample, the researchers identified on average 3,721 protein groups based on 25,699 peptides, and using 10 ng they identified 2,042 protein groups based on 11,424 peptides.


Journal: Journal of Proteome Research, June 16 [Epub]

Title: Additional precursor purification in isobaric mass tagging experiments by traveling wave ion mobility separation (TWIMS).

Authors: Shliaha PV, Jukes-Jones R, Christoforou A, Fox J, Hughes C, Langridge J, Cain K, Lilley KS.

The authors used traveling wave ion mobility separation to reduce precursor interference in shotgun mass spec, finding that it reduced signal-to-noise for sequence ions by an average of 2.85-fold.


Journal: Journal of Proteomics, June 26 [Epub ahead of print]

Title: A Candida albicans PeptideAtlas.

Authors: Vialas V, Sun Z, Loureiro y Penha CV, Carrascal M, Abián J, Monteoliva L, Deutsch EW, Aebersold R, Moritz RL, Gil C.

The authors present the Candida albicans PeptideAtlas comprising 22,000 distinct peptides that can be used for protein and peptide searching as well as for choosing candidate peptides for targeted proteomic measurements. According to the authors, it is the first representative of a fungal pathogen in PeptideAtlas and the most comprehensive characterization of the organism to date.


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

Title: The C-score: a Bayesian framework to sharply improve proteoform scoring in high-throughput top down proteomics.

Authors: LeDuc RD, Fellers RT, Early BP, Greer JB, Thomas PM, Kelleher NL.

The authors present a Bayesian approach to identifying proteoforms in top-down proteomics that allows for the inclusion of expert knowledge into identification models. Applying the system to a manually curated set of 295 human proteoforms, the approach provided significant improvements over current models.


Journal: Proteomics, July 9 [Epub ahead of print]

Title: Rapid and sensitive profiling and quantification of the human cell line proteome by LC-MS/MS without prefractionation.

Authors: Yin X, Liu X, Zhang Y, Yan G, Wang F, Lu H, Shen H, Yang P.

The authors present a one-dimensional LC-MS/MS workflow capable of identifying 4,500 proteins from a human cell line using a gradient of less than eight hours. Applying it to an analysis of MLN4924 treated/untreated human umbilical vein endothelial cell samples with label-free quantification, they identified a total of 179 proteins showing a statistically significant expression change.


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

Title: Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis.

Authors: Kelkar DS, Provost E, Chaerkady R, Muthusamy B, Manda SS, Subbannayya T, Selvan LD, Wang CH, Datta KK, Woo S, Dwivedi SB, Renuse S, Getnet D, Huang TC, Kim MS, Pinto SM, Mitchell CJ, Madugundu AK, Kumar P, Sharma J, Advani J, Dey G1, Balakrishnan L, Syed N, Nanjappa V, Subbannayya Y, Goel R, Prasad TS, Bafna V, Sirdeshmukh R, Gowda H, Wang C, Leach SD, Pandey A.

The authors performed a proteogenomics analysis of zebrafish, identifying more than 7,000 proteins as well as 157 novel protein-coding genes. Additionally they identified four cases of genome assembly errors.

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