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Recent Research Papers of Note in Proteomics: Jun 28, 2007

Journal: The Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society, July
Title: Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens
Authors: T Guo; W Wang; PA Rudnick; T Song; J Li; Z Zhuang; RJ Weil; DL Devoe; CS Lee; BM Balgley
Authors used combined capillary isoelectric focusing/nano-reverse-phase LC separations, equipped with nano-electrospray ionization-tandem MS, to study proteins extracted from microdissected formalin-fixed and paraffin-embedded glioblastoma tissues using a heat-induced antigen retrieval technique. They identified 14,478 distinct peptides, leading to the identification of 2,733 non-redundant SwissProt protein entries.

Journal: BMC Bioinformatics, June 21 [Epub ahead of print]
Title: Precise protein quantification based on peptide quantification using iTRAQ
Authors: AM Boehm; S Puetz; D Altenhofer; A Sickmann; M Falk
Authors describe a method for calculating reliable quantification information. It comprises sound error estimation and statistical methods, and allows for precise abundance analysis and error calculation at the peptide, as well as protein level. They say their method, named Quant, demonstrates improvements over iTRAQ

Journal: Analytical Chemistry, June 20 [Epub ahead of print]
Title: Reproducibility assessment of relative quantitation strategies for LC-MS based proteomics
Authors: YJ Kim; P Zhan; B Field; SM Ruben; T He
Authors present a reproducibility assessment method for relative quantitation based on the intensity ratio distribution of common features in LC-MS replicates. The method applies to label-free quantitation and label-dependent quantitation methods.

Journal: Analytical Chemistry, June 16 [Epub ahead of print]
Title: Dynamic collision-induced dissociation of peptides in a quadrupole ion trap mass spectrometer
Authors: OL Collin; M Beier; GP Jackson
Authors demonstrate the utility of dynamic collision-induced dissociation for fragmenting natural peptides. The method is novel for quadrupole ion traps, they say. The authors use leucine enkephalin as a diagnostic molecule and compare the fragmentation efficiencies and energetics of DCID with other methods of collisional activation in ion traps such as conventional on-resonance excitation and high-amplitude short-time excitation.

Journal: Journal of Chromatography B, Analytical Technologies in the Biomedical and Life Sciences, June 15
Title: High throughput LC-MS/MS method for simultaneous quantification of lamivudine, stavudine, and nevirapine in human plasma
Authors: HN Mistri; AG Jangid; A Pudage; N Gomes; M Sanyal; P Shrivastav
Authors developed a selective, high-throughput LC-MS/MS method to separate, detect and quantify lamivudine, stavudine, and nevirapine in human plasma. Metaxalone is used as the internal standard.

Journal: Proteomics, June 14 [Epub ahead of print]
Title: The PSI formal document process and its implementation on the PSI website
Authors: JA Vizcaino; L Martens; H Hermjakob; RK Julian; NW Paton
The Human Proteome Organization’s Proteomics Standards Initiative recently developed formal document processes for reviewing MIAPE documents, specifications, community practice, and informal documents. Here, the authors present the web interface used to support the document workflows, and explain how interested parties can participate in the review process.

Journal: BMC Bioinformatics, June 13 [Epub ahead of print]
Title: MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data
Authors: J Hartler; GG Thallinger; G Stocker; A Sturn; TR Burkard; E Korner; R Rader; A Schmidt; K Mechtler; Z Trajanoski
Authors describe a new platform they developed for managing the large amount of information contained in proteomic datasets. Called MAss SPECTRometry Analysis System, the platform is based on the Proteome Experimental Data Repository relational database schema and follows the guidelines of the Human Proteome Organization’s Proteomics Standards Initiative. Analysis modules include import and parsing of the results from the search engines Sequest, Mascot, Spectrum Mill, X! Tandem, and OMSSA; peptide validation; clustering of proteins based on Markov Clustering and multiple alignments; and quantifications using the Automated Statistical Analysis of Protein Abundance Rations algorithm.

Journal: Journal of Proteome Research, June 12 [Epub ahead of print]
Title: Analysis of signaling pathways in 90 cancer cell lines by protein lysate array
Authors: KN Mendes; D Nicorici; D Cogdell; I Tabus; O Yli-Harja; R Guerra; SR Hamilton; W Zhang
Authors assembled a protein lysate array with 90 different line cells of 12 different cell types. The purpose is to determine whether common signal transduction pathways are ubiquitously altered in all cancer types and some unique pathways are involved in different cancer types; and whether and how transduction signaling molecules are heterogeneously expressed and activated in different cancer cells within and between cancer cell types.

Journal: Molecular & Cellular Proteomics: MCP, June 12 [Epub ahead of print]
Title: Quantitative profile of five murine core proteomes using label-free functional proteomics
Authors: PR Cutillas, B Vanhaesebroeck
Authors developed a computational program and normalization procedures for relative and absolute quantification of proteins in complex mixtures, using the quantitative data inherent in LC-MS/MS experiments. Features of their approach include the ability to compare an unlimited number of samples; its applicability to primary tissues and cultured cells; and its straightforward workflow without chemical reaction steps.

Journal: Biochemical and Biophysical Research Communications, June 8
Title: A proteomics approach to identify the ubiquitinated proteins in mouse heart
Authors: HB Jeon: ES Choi; HJ Yoon; JH Hwang; JW Chang; EK Lee; HW Choi; ZY Park; YJ Yoo
Authors generated a transgenic mouse expressing a tagged ubiquitin in the heart. A majority of the ubiquitinated proteins in the mouse heart were chemically cleaved after methionine with CNBr. Ubiquitin-conjugated polypeptides were purified under denaturing conditions, and digested with Lys-C and trypsin. Analysis by LC-MS/MS identified 121 proteins ubiquitinated in the mouse heart and 33 ubiquitination sites in 21 of the proteins. Their study, the authors say, suggests that major heart functions such as contraction and energy production are under continuous quality control of the ubiquitin system.

Journal: Journal of Proteome Research, June 7 [Epub ahead of print]
Title: Proteomic profiling of plasma in Huntington’s disease reveals neuroinflammatory activation and biomarker candidates
Authors: A Dalrymple; EJ Wild; R Joubert; K Sathasivam; M Björkqvist; A Petersén; GS Jackson; JD Isaacs; M Kristiansen; GP Bates; BR Leavitt; G Keir; M Ward; SJ Tabrizi
Authors used multiplatform proteomic profiling to detect plasma changes with Huntington’s disease progression. They used immunoblotting and ELISA in plasma to evaluate proteins of interest. The identified proteins demonstrate neuroinflammation in HD and warrant further research as possible biomarkers, they say in their abstract.

Journal: Analytical Chemistry, June 6 [Epub ahead of print]
Title: MSNovo; A dynamic programming algorithm for de novo peptide sequencing via tandem mass spectrometry
Authors: L Mo; D Dutta; Y Wan; T Chen
Authors say their new approach to peptide de novo sequencing, MSNovo, works on data generated from LCQ and LTQ MS and interprets singly, doubly, and triply charged ions. The approach also integrates a new probabilistic scoring function with mass array-based dynamic programming algorithm, avoiding the problem of overfitting and allowing MSNovo to be adopted for other machines and data sets easily. The authors say MSNovo predicts peptides and sequence tags with greater accuracy than other programs.

Journal: Proteome Science, June 6, 2007
Title: PrestOMIC, an open source application for dissemination of proteomic datasets by individual laboratories
Authors: CG Howes; LJ Foster
Authors present PrestOMIC, an open source application for storing MS-based proteomic data in a relational database and for providing a “user-friendly, searchable, and customizable browser interface to share one’s data with the scientific community,” they say in the abstract. The underlying database and associated applications are built on other open source tools, so PrestOMIC can be modified as data standards change, the authors say.

Journal: Journal of Proteome Research, June 6 [Epub ahead of print]
Title: Identification of proteolytic cleavage sites by quantitative proteomics
Authors: M Enoksson; J Li; MM Ivancic; JC Timmer; E Wildfang; A Eroshkin; GS Salvesen; WA Tao
Authors describe a new strategy for identifying signature proteolytic cleavage events based on quantitative proteomics. Lysine residues in proteins are blocked by guanidination so that free N-terminals can be labeled with amine specific iTRAQ reagents. Proteins are tryptically digested, then analyzed via MALDI-TOF-TOF MS. Peptides labeled with iTRAQ are distinguished from other peptides by “exhibiting intense signature ions in tandem mass spectrometry analysis,” according to the abstract.

Journal: Nucleic Acids Research, June 6 [Epub ahead of print]
Title: The Multi-Q web server for multiplexed protein quantitation
Authors: CY Yu; YH Tsui; YH Yian; TY Sung; WL Hsu
According to the abstract, the Multi-Q web server is an automated data analysis tool for multiplexed protein quantitation based on the iTRAQ labeling method. Compared to the previous stand-alone version, the new web server has more enhanced features and flexible options for quantitation.

Journal: Journal of Proteome Research, June 6
Title: Characterization of phosphorylation sites on Tpl2 using IMAC enrichment and a linear ion trap mass spectrometer
Authors: TM Black, CL Andrews; G Kilili; M Ivan; PN Tsichlis; P Vouros
Tumor progression locus 2 has been implicated in cell cycle regulation and shown to play a role in critical signal transduction pathways. Authors transfected Tppl2 into 293T cells, overexpressed and isolated from the cell lysate. Isolated proteins were separated by 1D gel electrophoresis. Phosphorylation was confirmed using phosphospecific staining. The bands were then excised and subjected to tryptical digestion and immobilized metal affinity chromatography prior to analysis by capillary-LC-MS/MS. Three phosphorylation sites were detected on Tpl2, including two novel sites.

Journal: Journal of Proteome Research, June 6
Title: A new algorithm using cross-assignment for label-free quantitation with LC-LTQ-FT MS
Authors: VP Andreev; L Li; L Cao; Y Gu; T Rejtar; SL Wu; BL Karger
Authors describe a new algorithm, Q-MEND, for label-free quantitation of relative protein abundances across multiple complex proteomic samples. In the approach, all MS/MS identifications for the sets of analyzed samples are combined into a master identification list. Each LC-MS run is searched for features that that can be assigned to a specific identification from the master list.

Journal: Proteomics, June 5 [Epub ahead of print]
Title: A protein chip approach for high-throughput antigen identification and characterization
Authors: S Hu; Y Li; Q Song; L Wang; Y Han; Y Zhang; Y Song; X Yao; Y Tao; H Zeng; H Yang; J Wang; H Zhu; ZN Chen; L Wu
Authors report a new approach for producing monoclonal antibodies against human liver proteins using a combined force of high-throughput mAb production and protein microarrays.

Journal: Proteomics, June 5, [Epub ahead of print]
Title: A multivariate analysis approach to the integration of proteomic and gene expression data
Authors: A Fagan; AC Culhane; DG Higgins
Authors apply co-inertia analysis, a multivariate statistical method, to visualize gene and proteomic expression data stemming from the same biological samples. After analysis is done on single datasets, CIA is used to explore the relationships between two or more datasets. Gene-ontology information is projected onto these plots to describe the cellular processes in action. The techniques are applied to gene expression and protein abundance data from studies of the human malarial parasite life cycle and the NCI-60 cancer cell lines.

Journal: Biochemical and Biophysical Research Communications, June 1
Title: Alignment of two-dimensional electrophoresis gels
Authors: G Shi; T Jian; W Zhu; B Liu; H Zhao
Authors propose a novel iterative closest point method for 2D-gel electrophoresis image alignment. “The paper seeks to introduce an information theoretic measure as one part of distance metric to gel image alignment,” according to the abstract.

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