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Recent Research Papers of Note in Proteomics: Dec 20, 2007

Journal: Nature Methods, Dec. 16 [Epub ahead of print]
Title: A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli
Authors: CS Chen; K Korobkova; H Chen; J Zhu; X Jian; SC Tao; C He; H Zhu
Authors describe a protocol for high-throughput protein purification that allowed them to purify 4,256 proteins encoded by E. coli K12 strain within 10 hours. The purified proteins were spotted onto glass slides to create E. coli proteome chips. Authors used the chips to develop assays for identifying proteins involved in the recognition of potential base damage in DNA.

Journal: Journal of Proteome Research, Dec. 14 [Epub ahead of print]
Title: Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling
Authors: H Choi; D Ghosh; AI Nesvizhskii
Authors present two flexible methods that remove the restrictive parametric assumptions in the mixture modeling approach of PeptideProphet, a computational tool used for assessing the statistical confidence in peptide assignments in tandem mass spectra obtained using database search programs. The two methods proposed are the variable component mixture model and the semiparametric mixture model.

Journal: Journal of Chromatography. A, Dec. 10 [Epub ahead of print]
Title: Toward chromatographic analysis of interacting protein networks
Authors: X Liu; WC Yang; Q Gao; F Regnier
Authors investigate the feasibility of taking chromatographic methods used in the preparative isolation of native proteins and incorporating them into global proteomics methods so that the primary structure of protein complexes stable enough to survive chromatography could be recognized along with their participation in protein complexes.
Size-exclusion chromatography was incorporated into all the fractionation strategies examined. Authors also examined anion-exchange chromatography and hydrophobic-interaction chromatography. The authors concluded that “protein complexes could be incorporated into multidimensional methods for global proteomics when at least one of the fractionation dimension included [size-exclusion chromatography] of native proteins,” according to the abstract.

Journal: Proteomics, Dec. 10 [Epub ahead of print]
Title: The significance of biochemical and molecular sample integrity in brain proteomics and peptidomics: Stathmin 2-20 and peptides as sample quality indicators
Authors: K Sköld, M Svensson; M Norrman; B Sjögren; P Svenningsson; PE Andrén
Authors show that proteins and neuropeptides, including their post-translational modifications undergo massive degradation in the brain, even after one minute post-mortem. They further identified markers for determining the integrity and status of a biological sample. They say the protein fragment stathmin 2-2i “correlated well with the general level of post-mortem degradation and may serve as a sample quality indicator for future work.” Lastly, they present a novel method for preventing the degradation of proteins and peptides in post-mortem tissue. The method uses rapid and uniform conductive heat transfer on tissue before sample preparation.

Journal: Journal of Proteome Research, Dec. 8 [Epub ahead of print]
Title: Clustering millions of tandem mass spectra
Authors: AM Frank; N Bandeira; Z Shen; S Tanner; SP Briggs; RD Smith; PA Pevzner
Authors present a clustering approach for analyzing MS/MS datasets containing more than 10 million spectra. The approach has the capability of reducing an order of magnitude the number of spectra submitted for further analysis.

Journal: Briefings in Bioinformatics, Dec. 7 [Epub ahead of print]
Title: The HUPO proteomics standards initiative easing communication and minimizing data loss in a changing world
Authors: S Orchard; H Hermjakob
Authors provide an update on the progress of the HUPO PSI group to create data standards and interchange formats.

Journal: Proteomics, Dec. 7
Title: Two-dimensional separation of human plasma proteins using iterative free-flow electrophoresis
Authors: M Nissum; S Kuhfuss; M Hauptmann; C Obermaier; U Sukop; R Wildgruber; G Weber; C Eckerskorn; J Malmström
A novel separation method using 2D free-flow electrophoresis presented. The approach separates proteins and peptides in solution according to their isoform prior to LC-MS/MS. The authors say the approach revealed low-abundant proteins and several tissue leakage products, “thus providing a powerful orthogonal separation step in the proteomics workflow.”

Journal: Proteomics, Dec. 7
Title: A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments
Authors: J Grossmann; B Fischer; K Baerenfaller; J Owiti; JM Buhmann; W Gruissem; S Baginsky
Authors present and evaluate a strategy for MS identification of proteins from organisms for which no genome sequence information is available. The approach incorporates cross-species information from sequenced organisms, and combines spectrum quality scoring, de novo sequencing, and error tolerant BLAST searches. The strategy is designed to decrease input data complexity.

Journal: Journal of Proteome Research, Dec. 4 [Epub ahead of print]
Title: A data-mining scheme for identifying peptide structural motifs responsible for different MS/MS fragmentation intensity patterns
Authors: Y Huang; GC Tseng; S Yuan; L Pasa-Tolic; MS Lipton; RD Smith; VH Wysocki
Authors describe a knowledge mining approach to discover fragmentation intensity patterns and to elucidate the chemical factors behind such patterns.

Journal: Journal of Proteome Research, Dec. 1 [Epub ahead of print]
Title: Real-time fluorescence monitoring of tryptic digestion in proteomics
Authors: P Karuso; AS Crawford; DA Veal; GB Scott; HY Choi
A new method is presented for monitoring protein digestion, based on epicocconone, a natural fluorphore that reacts reversibly with proteins to form a highly fluorescent adduct. The in situ assay can “tracelessly follow proteolysis of samples, at low microgram levels, destined for proteomics analysis or purification,” the authors say.

Journal: Electrophoresis, December
Title: Chip-LC-MS for label-free profiling of human serum
Authors: P Horvatovich; NI Govorukhina; TH Reijmers; AG van der Zee; F Suits; R Bischoff
Authors apply a microfluidics-based LC-MS system to the label-free profiling of immunodepleted, trypsin-d
igested serum in comparison to conventional capillary LC-MS. According to them, the chip-LC-MS system had a two times higher resolution in the LC dimension and resulted in a lower average charge state of the tryptic peptide ions generated in the electrospray ionization interface, compared to cap-LC-MS while requiring 30 times less sample.

Journal: Journal of Proteome Research, Nov. 30 [Epub ahead of print]
Title: Design of recombinant antibody microarrays for cell surface membrane proteomics
Authors: L Dexlin; J Ingvarsson; B Frendeus; CA Borrebaeck; C Wingren
Authors designed the first generation of a scaleable human recombinant scFv antibody microarray technology platform for cell surface membrane proteomics and glycomics targeting intact cells. From their work, the results show that “rapid and multiplexed profiling of the cell surface proteome could be performed in a highly specific and sensitive manner and that differential expression patterns due to external stimuli could be monitored,” the authors say.

Journal: Analytical Chemistry, Nov. 29 [Epub ahead of print]
Title: Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses
Authors: EA Livesay; K Tang; BK Taylor; MA Buschbach; DF Hopkins; BL Lamarche; R Zhao; Y Shen; DJ Orton; RJ Moore; RT Kelly; HR Udseth; RD Smith
Authors have devised a four-column, high pressure capillary LC system that performs multiple LC separations in parallel. Each separation is staggered in a way so that the data-rich region of each separation is sampled sequentially. “By allowing nearly continuous data acquisition, this design maximizes the use of the mass spectrometer,” they say in the abstract.

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