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Recent Research Papers of Note in Proteomics: Nov 29, 2007

Journal: Cytometry Part A: The Journal of the International Society for Analytical Cytology, December
Title: Automated learning of generative models for subcellular location: Building blocks for systems biology
Authors: T Zhao; RF Murphy
Authors previously developed automated quantitative methods for identifying protein subcellular location families. However, there was no way to communicate their patterns to integrate them with other information for building cell models. Here, they describe generative models of subcellular location that are learned from a collection of images so that they represent a pattern while also capturing its variation from cell to cell.

Journal: Protein Science: A Journal of the Protein Society, Dec. 16
Title: A rapid and universal tandem-purification strategy for recombinant proteins
Authors: AJ McCluskey; GM Poon; J Gariepy
Authors report the design and use of a novel tandem (His)(6)-calmodulin (HiCaM) fusion tag combining two distinct purification strategies, immobilized metal affinity and hydrophobic interaction chromatography, in a two-step procedure.

Journal: Nucleic Acids Research, Nov. 22 [Epub ahead of print]
Title: PRIDE: new developments and new datasets
Authors: P Jones; RG Cote; SY Cho; S Klie; L Martens; AF Quinn; D Thorneycroft; H Hermjakob
Since PRIDE was described in the NAR Database Special Edition a year ago, the volume of public data in the PRIDE relational database has grown by more than an order of magnitude, and several significant public datasets have been added, including identifications and processed mass spectra generated by the Human Proteome Organization’s Brain Proteome Project and Liver Proteome Project. The software development team for PRIDE has made significant changes and additions to the user interface and tool set associated with PRIDE, according to the authors.

Journal: Bioinformatics, Nov. 22 [Epub ahead of print]
Title: Fast and accurate identification of semi-tryptic peptides in shotgun proteomics
Authors: P Alves; RJ Arnold; DE Clemmer; JP Reilly: Q Sheng; H Tang; Z Xun; R Zeng; P Radivojac
In shotgun proteomics, identifying all potential non-tryptic peptides is time consuming and poses a challenge for routine data analysis. Authors hypothesize that non-tryptic peptides are mainly created from the truncation of regular tryptic peptides, and build a predictor to estimate a peptide’s truncatability from its sequence.

Journal: Molecular & Cellular Proteomics, Nov. 19 [Epub ahead of print]
Title: Statistical similarities between transcriptomics and quantitative shotgun proteomics data
Authors: N Pavelka; ML Fournier; SK Swanson; M Pelizzola; P Ricciardi-Castagnoli; L Florens; MP Washburn
Authors analyze two large multi-dimensional protein identification technology datasets to determine whether normalized spectral abundance factor values share significantly similar statistical properties with transcript abundance values from Affymetrix GeneChip data. The purpose is to determine whether the large collection of microarray-specific statistical tools is applicable to the analysis of quantitative shotgun proteomics datasets.

Journal: Analytical Chemistry, Nov. 17 [Epub ahead of print]
Title: Peptide sequencing and characterization of post-translational modifications by enhanced ion-charging and liquid chromatography electron-transfer dissociation tandem mass spectrometry
Authors: F Kjeldsen; AM Giessing; CR Ingrell; ON Jensen
Authors test the effect of m-nitrobenzyl alcohol to increase the average charge state of protonated gas-phase molecular ions generated by ESI from tryptic peptides and phosphopeptides.

Journal: European Journal of Biochemistry/FEBS, Nov. 16 [Epub ahead of print]
Title: Analysis of proteins and peptides on a chromatographic timescale by electron-transfer dissociation MS
Authors: ND Udeshi; J Shabanowitz; DF Hunt; KL Rose
Described is peptide and protein sequence analysis using combination gas-phase ion-ion chemistry and tandem-MS. Provided are also examples that demonstrate the utility of ETD for characterizing post-translational modifications and for identifying proteins in mixtures on a chromatographic timescale (500 ms/protein).

Journal: Analytical Chemistry, Nov. 15
Title: SDS–PAGE focusing: Preparative aspects
Authors: G Zilberstein; L Korol; PG Righetti; S Bukshpan
Authors report a novel method for small-scale prefractionation of complex protein mixtures and subsequent proteome analysis. The method is based on mass separation of SDS-protein micelles not in a gel matrix, but in liquid cationic polymers assembled in a multicompartment electrolyzer “in a stepwise fashion at discrete and increasing levels of positive charges … the neighboring chambers being separated by neutral agarose membranes,” according to the abstract.

Journal: Analytical Chemistry, Nov. 15 [Epub ahead of print]
Title: Enabling MALDI-FTICR-MS/MS for high-performance proteomics through combination of infrared and collisional activation
Authors: ED Dodds, JG German; CB Lebrilla
A recently developed MS/MS technique, dubbed combination of infrared and collisional activation, or CIRCA, is shown to be suitable for dissociating singly protonated tryptic peptides, “providing greater sequence coverage than either [collision-induced dissociation] or infrared multiphoton dissociation alone,” according to the abstract.

Journal: Analytical Chemistry, Nov. 15
Title: Rational selection of the optimum MALDI matrix for top-down proteomics by in-source decay
Authors: K Demeure; L Quinton; V Gabelica; ED Pauw
Authors present a “rational” way to select MALDI matrixes likely to enhance in-source decay for top-down proteomics. Using their approach, optimized matrix preparation was applied successfully for the identification of larger proteins by large ISD tag researches in protein databases, and coupled with adequate separation methods, ISD is a “promising” tool in top-down proteomics, they say.

Journal: Bioinformatics, Nov. 15
Title: Leveraging the structure of the semantic web to enhance information retrieval for proteomics
Authors: A Smith; K Cheung; M Krauthammer; M Schultz; M Gerstein
To enable quick retrieval of relevant information from the web and biomedical literature, authors developed an approach joining the semantic web with the “largely opposing paradigm of unsupervised web search,” according to the abstract.

Journal: Journal of Proteome Research, Nov. 15 [Epub ahead of print]
Title: The effects of shared peptides on protein quantitation in label-free proteomics by LC-MS/MS
Authors: S Jin; DS Daly; DL Springer; JH Miller
Described is an approach for including shared peptides in the analysis of differential protein abundance in protein profiling. They used data from recent proteomics studies on the effect of lipopolysaccharide, cigarette smoke, and a combination of these agents on mice to illustrate their method. Starting with data where half of the implicated database protein involved shared peptides, 82 percent of the affected proteins were grouped into families, based on FASTA annotation with closure on peptide sharing. Based on their results, they propose that “peptide-sharing closure groups provide a means for including abundance data for shared peptides in quantitative protein profiling by high-throughput mass spectrometry.”

Journal: Analytical Chemistry, Nov. 14 [Epub ahead of print]
Title: LC-MS/MS approach for quantification of therapeutic proteins in plasma using a protein internal standard and 2D-solid-phase extraction cleanup
Authors: Z Yang; M Hayes; X Fang; MP Daley; S Ettenberg; FL Tse
An LC-MS/MS bioassay was developed for the quantification of somatropin and a therapeutic human monoclonal antibody as a strategy to enable bioanalysis of plasma samples in a timely and accurate manner. Authors say that compared to a conventional ELISA approach, their approach improved accuracy and precision.

Journal: Bioinformatics, Nov. 14 [Epub ahead of print]
Title: Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra
Authors: D Mantini; F Petrucci; PD Boccio; D Pieragostino; MD Nicola; A Lugaresi; G Federici; P Sacchetta; CD Ilio; A Urbani
Authors propose independent component analysis as a method for the analysis of signals from large proteomics investigations.

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