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In Print: Recent Proteomics Papers of Note: May 30, 2014

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In Print: Recent Proteomics Papers of Note

Journal: PLOS One, April 7

Title: Top-down proteomics with mass spectrometry imaging: A pilot study towards discovery of biomarkers for neurodevelopmental disorders.

Authors: Ye H, Mandal R, Catherman A, Thomas PM, Kelleher NL, Ikonomidou C, Li L.

The authors used MALDI mass spec imaging to analyze changes in protein expression in rats following neonatal exposure to the NMDA receptor antagonist dizocilpine, identifying changes in abundance in several proteins and demonstrating the utility of imaging mass spec for biomarker discovery.


Journal: Molecular & Cellular Proteomics, April 10 [Epub ahead of print]

Title: Immuno-proteomics using polyclonal antibodies and stable isotope labeled affinity-purified recombinant proteins.

Authors: Edfors F, Boström T, Forsström B, Zeiler M, Johansson H, Lundberg E, Hober S, Lehtiö J, Mann M, Uhlen M.

The authors present immuno-SILAC, a method for quantitative proteomics that combines antibody-based peptide enrichment with SILAC mass spec for multiplexed protein quantitation.


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

Title: Association of N-glycosylation with breast carcinoma and systemic features using high-resolution quantitative UPLC.

Authors: Saldova R, Asadi Shehni A, Haakensen VD, Steinfeld I, Hilliard M, Kifer I, Helland A, Yakhini Z, Børresen-Dale AL, Rudd PM.

The authors present an improved separation method for human serum N-glycoproteins using hydrophilic interaction chromatography. Using the technique they profiled samples from 107 health controls and 62 breast cancer patients, identifying significant differences in the serum N-glycomes of the two groups.


Journal: Nature Biotechnology, April 13 [Epub ahead of print]

Title: Proteome labeling and protein identification in specific tissues and at specific developmental stages in an animal.

Authors: Elliott TS, Townsley FM, Bianco A, Ernst RJ, Sachdeva A, Elsässer SJ, Davis L, Lang K, Pisa R, Greiss S, Lilley KS, Chin JW.

The authors introduce a technique, stochastic orthogonal recoding of translation with chemoselective modification (SORT-M), for labeling cells with unnatural amino acids in rich media at specific developmental stages and in specific tissues.


Journal: Journal of Proteomics, April 22 [Epub ahead of print]

Title: PeptidePicker: A scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments.

Authors: Mohammed Y, Domanski D, Jackson AM, Smith DS, Deelder AM, Palmblad M, Borchers CH.

The authors present an algorithm for identifying the most appropriate surrogate peptides for MRM-MS analysis based on information about the proteins, their tryptic peptides, and the suitability of the peptides for MRM analysis taken from resources including UniProtKB, NCBI's dbSNP, ExPASy, PeptideAtlas, PRIDE, and GPMDB. Using the software, the researchers were able to select peptides for roughly 50 proteins per hour, compared to 8 per day using conventional methods.


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

Title: Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness.

Authors: Liu Y, Chen J, Sethi A, Li QK, Chen L, Collins B, Gillet LC, Wollscheid B, Zhang H, Aebersold R.

The authors used SWATH mass spec to analyze N-linked glycopeptides from normal prostate, non-aggressive prostate tumors, aggressive tumors, and prostate cancer metastases, identifying NAAA and PTK7 as markers for aggressive forms of the disease.


Journal: Analytical and Bioanalytical Chemistry, April 24 [Epub ahead of print]

Title: High-throughput absolute quantification of proteins using an improved two-dimensional reversed-phase separation and quantification concatemer (QconCAT) approach.

Authors: Wei J, Ding C, Zhang J, Mi W, Zhao Y, Liu M, Fu T, Zhang Y, Ying W, Cai Y, Qin J, Qian X.

The authors present a targeted proteomics workflow using two-dimensional reversed-phase chromatography and quantification concatemers for the simultaneous quantification of hundreds of proteins in tissue samples. Using a 72-minute gradient in the first LC dimension, the researchers generated 72 fractions, the analysis of which they completed in one week while achieving improvements in sensitivity and dynamic range.


Journal: Journal of Proteome Research, April 29 [Epub ahead of print]

Title: Functional annotation of proteome encoded by human chromosome 22.

Authors: Pinto SM, Manda SS, Kim MS, Taylor K, Selvan LD, Balakrishnan L, Subbannayya T, Yan F, Prasad TS, Gowda H, Lee C, Hancock WS, Pandey A.

Working as part of the Human Proteome Organization's chromosome-centric human proteome project, the authors present an analysis of chromosome 22. Based on profiling of 30 normal tissues and cells using mass spectrometry, they generated protein evidence of 367 genes on this chromosome, including 47 proteins for which there had not previously been evidence.

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