In Print: Recent Proteomics Papers of Note
Journal: Nature Reviews Genetics, Dec. 4 [Epub ahead of print]
Title: Next-generation proteomics: towards an integrative view of proteome dynamics.
Authors: Altelaar AF; Munoz J; Heck AJ.
The authors provide an overview of what they call the "next generation of proteomics," citing developments in proteomic instrumentation, sample prep, and computational analysis and offering examples of recent applications.
Journal: Frontiers in Plant Science, Dec. 6 [Epub ahead of print]
Title: UniProtKB amid the turmoil of plant proteomics research.
Authors: Schneider M; Consortium TU; Poux S.
The authors detail the current status of the UniProt database as it relates to plant proteomics, noting a particular challenge the system faces in storing and organizing data on different cultivars of a given species and in clearly defining reference proteomes.
Journal: PLoS Computational Biology, Dec. 8 [Epub ahead of print]
Title: A universal trend among proteomes indicates an oily last common ancestor.
Authors: Mannige RV; Brooks CL; Shakhnovich EI.
The authors present data across 272 diverse proteomes indicating a steady decline in proteome hydrophobicity, an observation they say indicates an inherent irreversibility in molecular evolution and could prove important for purposes including explaining the emergence of intrinsically disordered proteins and improving methods of ancestral sequence reconstruction.
Journal: Journal of Proteome Research, Dec. 13 [Epub ahead of print]
Title: Tryptic peptide reference data sets for MALDI imaging mass spectrometry on formalin-fixed ovarian cancer tissues.
Authors: Meding S; Martin K; Gustafsson OJ; Eddes JS; Hack S; Oehler MK; Hoffmann P.
The authors used LC-MS/MS to analyze tryptic digests of FFPE tissue from 31 ovarian cancer patients in order to crease a reference database for use in MALDI imaging experiments in ovarian cancer. They identified 3,844 distinct peptide sequences for the entire cohort, for a total of 840 proteins.
Journal: Nature Communications, Dec. 18
Title: Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes.
Authors: Karlsson C, Malmström L, Aebersold R, Malmström J.
The authors developed a set of SRM mass spec assays for 10,412 Streptococcus peptides and developed a scoring system to evaluate the best assays for each protein given a particular cellular compartment and bacterial state.
Journal: Proceedings of the National Academy of Sciences, Dec. 24 [Epub ahead of print]
Title: Proteome-wide protein interaction measurements of bacterial proteins of unknown function.
Authors: Meier M; Sit RV; Quake SR.
The authors present a physical protein interaction map developed by measuring the biophysical interaction of Streptococcus pneumoniae proteins using a microfluidic high-throughput assay technology. Using this approach they were able to assign putative functions to 50 proteins of unknown function.
Journal: Clinical Proteomics, Dec. 27
Title: Ovarian cyst fluid is a rich proteome resource for detection of new tumor biomarkers.
Authors: Kristjansdottir B; Partheen K; Fung ET; Marcickiewicz J; Yip C; Brännström M; Sundfeldt K.
The authors used mass spectrometry to analyze ovarian cyst fluid from 192 women, identifying a panel consisting of the proteins ApoC-III, PCI, and serum CA125 that identified epithelial ovarian cancer with ROC AUC of .94.
Journal: Journal of Proteome Research, Dec. 31 [Epub ahead of print]
Title: Contribution of antibody-based protein profiling to the Human Chromosome-centric Proteome Project (C-HPP)
Authors: Fagerberg L; Oksvold P; Skogs M; Algenäs C; Lundberg E; Pontén F; Sivertsson A; Odeberg J; Klevebring D; Kampf C; Asplund A; Sjöstedt E; Al-Khalili Szigyarto C; Edqvist PH; Olsson I; Rydberg U; Hudson P; Ottosson Takanen J; Berling H; Björling L; Tegel H; Rockberg J; Nilsson P; Navani S; Jirström K; Mulder J; Schwenk JM; Zwahlen M; Hober S; Forsberg M; von Feilitzen K; Uhlén M.
The authors report on protein evidence for all genes predicted from the human genome sequence based on annotation in UniProt, antibody-based profiling, and transcript analysis, finding good evidence for proteins for 69 percent of the human protein coding genes, with 23 percent having evidence only on the RNA level, and 7 percent lacking experimental evidence.