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Recent Research Papers of Note in Proteomics: Sep 6, 2007

Journal: Analytical Biochemistry, Sept. 15
Title: Protein identification by syringe pump-driven reversed-phase LC-MS/MS
Authors: CY Lu; Cy Wu; CH Lin
Authors describe a separation method based on a simple nanoflow delivery system that is able to shorten the separation time. The system includes a 25-microliter syringe connected to a manually packed reversed-phase mini-capillary column that can be coupled directly to an electrospray ionization MS/MS.

Journal: Frontiers in Bioscience : A Journal and Virtual Library, Sept. 1
Title: Integration of bioinformatics resources for functional analysis of gene expression and proteomic data
Authors: H Huang; ZZ Hu; CN Arighi; CH Wu
Authors describe a central data infrastructure, iProClass, which supports both data integration and functional annotation of proteins, and introduce IProXpress, an integrated research and discovery platform for large-scale expression data analysis.

Journal: Bioinformatics, Aug. 25 [Epub ahead of print]
Title: MeTaDoR: A comprehensive resource for membrane targeting domains and their host proteins.
Authors: N Bhardwaj; RV Stahelin; G Zhao; W Cho; H Lu
Authors created MeTaDoR, “a comprehensive resource dedicated to membrane targeting domains.” The resource is available here.

Journal: Bioinformatics, Aug. 24, [Epub ahead of print]
Title: PARE: A tool for comparing protein abundance and mRNA expression data
Authors: EZ Yu; AE Counterman Burba; M Gerstein
Authors developed Protein Abundance and mRNA Expression, a web tool available here, to correlate protein abundance with mRNA expression data. PARE allows users to select subsets of proteins for focused studies and highlight correlation outliers, according to the authors.

Journal: Journal of Proteome Research, Aug. 21 [Epub ahead of print]
Title: The standard protein mix database: A diverse data set to assist in the production of improve peptide and protein identification software tools
Authors: J Klimek; JS Eddes; L Hohmann; J Jackson; A Peterson; S Letarte; PR Gafken; JE Katz; P Mallick; H Lee; A Schmidt; R Ossola JK Eng; R Aebersold; DB Martin
According to the authors, many software applications assigning probabilities for MS/MS spectra to sequence matches were developed using training datasets from 3D ion-trap MS. With greater availability of different types of MS, the authors “sought to generate a data set of reference data covering multiple instrumentation platforms to facilitate both the refinement of existing computational approaches and the development of novel software tools.”
They analyzed the proteolytic peptides in a mixture of tryptic digests of 18 proteins using eight different MS including linear and 3D ion traps, two quadrupole TOF, and two MALDI-TOF-TOF platforms.

Journal: Journal of Proteome Research, Aug. 21, [Epub ahead of print]
Title: Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer
Authors: JR Whiteaker; H Zhang; Lei Zhao; P Wang; KS Kelly-Spratt; RG Ivey; BD Piening; LC Feng; E Kasarda; Ke Gurley; JK Eng; LA Chodosh; CJ Kemp; MW McIntosh; AG Paulovich
Authors performed LC-MS/MS of tumor and normal mammary tissue from a conditional HER2/Neu-driven mouse model of breast cancer and identified 6,758 peptides representing more than 700 proteins. They developed a novel statistical approach, called SASPECT, to prioritize proteins differentially expressed in LC-MS/MS datasets and identified proteins over- or under-represented in tumors.
“Our results show that a staged pipeline employing shotgun-based comparative proteomics for biomarker discovery and multiple reaction monitoring for confirmation of biomarker candidates is capable of finding novel tissue and plasma biomarkers in a mouse model of breast cancer,” they say in the abstract. “Furthermore, the approach can be extended to find biomarkers relevant to human disease.”

Journal: Proteomics, Aug. 21 [Epub ahead of print]
Title: Implementation and application of a versatile clustering tool for tandem mass spectrometry data
Authors: K Flikka; J Meukens; K Helsens; J Vandekerckhove; L Eidhammer; K Gevaert; L Martens
Authors created a general purpose, open-source software application for clustering and merging MS/MS spectra and introduce a novel approach for calculating the similarity of fragmentation mass spectra that takes into account “the increased precision of modern mass spectrometers,” they say in the abstract.

Journal: Analytical Chemistry, Aug. 15
Title: Noncompetitve detection of low molecular weight peptides by open sandwich immunoassay
Authors: SL Lim; H Ichinose; T Shinoda; H Ueda
Authors tried noncompetitive detection of small peptides by open sandwich enzyme-linked immunosorbent assay, utilizing the antigen-induced enhancement of antibody VH/VL interaction. Their approach, which relies on a single monoclonal antibody with a short measurement time, “may prove a useful tool in immunodiagnostics, as well as in proteomics research,” according to the abstract.

Journal: Journal of Proteome Research, Aug. 7 [Epub ahead of print]
Title: An automated platform for analysis of phosphoproteomic datasets: Application to kidney collecting duct phosphoproteins
Authors: JD Hoffert; G Wang; T Pisitkun; RF Shen; MA Knepper
Authors created software, named PhosphoPeptide Identification and Compilation, to perform automated selection and compilation of phosphopeptide identifications from multiple MS levels, estimation of dataset false discovery rate, and application of appropriate cross correlation filters. The output files generated by the program are compatible with downstream phosphorylation site assignment using the Ascore algorithm, as well as phosphopeptide quantification via QUOIL. In the report, the authors applied the software for the analysis of phosphoproteins from short-term vasopressin-treated rat kidney inner collecting duct.

Journal: Journal of Separation Science, Aug. 7 [Epub ahead of print]
Title: Peptide correlation: A means to identify high quality quantitative information in large-scale proteomic studies
Authors: E Schwarz; Y Levin; L Wang; FM Leweke; S Bahn
Authors set out to show that “peptides that accurately reflect relative protein abundances in large-scale sample sets can be selected based on the correlation to each other.” They tested their strategy in an experiment using a set of spiked serum samples and 55 clinical serum samples from schizophrenia patients and healthy volunteers.

Journal: Proteomics, Aug. 6 [Epub ahead of print]
Title: Targeted protein quantitation and profiling using PVDF affinity probe and MALDI-TOF MS
Authors: SH Chen; HK Liao; CY Chang; CG Juo; JH Chen; SI Chan; YJ Chen
Authors describe a technique for protein quantitation and profiling that takes advantage of the natural hydrophobic interaction of PVDF with probe protein. They used antibody-antigen interactions as a proof-of-concept system and were able to selectively isolate and enrich targeted plasma proteins, serum amyloid P, serum amyloid A, and C-reactive protein from human plasma by antibody-immobolized PVDF membrane and directly identify them by MALDI-TOF MS without an additional elution step.

Journal: Journal of Proteome Research, Aug. 3
Title: Analysis of the mouse liver proteome using advanced mass spectrometry
Authors: R Shi; C Kumar; A Zougman; Y Zhang; A Podtelejnikov; J Cox; JR Wiœniewski; M Mann
Authors enriched two fractions of mouse liver tissue for soluble and membranes from 20 milligrams of frozen tissue. The fractions were then separated by 1D electrophoresis, followed by LC-MS/MS. They report confident identification of 2,210 proteins relying on at least two peptides. They combined this proteome with a previously reported organellar map to generate “very high confidence mouse liver proteome of 3,244 proteins,” according to the abstract. For potential toxicology and clinical studies, they say they demonstrate that it is possible to identify more than 1,000 proteins in a single run.

Journal: Journal of Separation Science, Aug. 2 [Epub ahead of print]
Title: Label-free LC-MS/MS quantitative proteomics for large-scale biomarker discovery in complex samples
Authors: Y Levin; E Schwarz; L Wang; FM Leweke; S Bahn
Authors used a set of spiked serum samples and a set of 55 clinical serum samples from schizophrenia patients and healthy volunteers to demonstrate that a label-free approach can yield reproducible results across a large number of samples and can be used to measure the relative protein abundance. Using this approach, they were able to identify 1,700 serum proteins covering a dynamic range of three orders of magnitude.

Journal: Analytical Chemistry, Aug. 1
Title: High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics datasets using high-resolution mass spectrometry
Authors: MR Hoopmann; GL Finney; MJ Maccoss
Authors report an algorithm called Hardklör for the rapid and robust analysis of high-resolution mass spectra generated from shotgun proteomics experiments. They demonstrate the use of the algorithm in an analysis of E. coli.

Journal: Analytical Chemistry, Aug. 1
Title: Reproducibility assessment of relative quantitation strategies for LC-MS based proteomics
Authors: YJ Kim; P Zhan; B Feild; SM Ruben; T He
Authors report a method for assessing the reproducibility of relative quantitation. The method is based on the intensity ratio distribution of common features in LC-MS replicates and applies to both decoupled and coupled methods. The authors note that the ratio distribution of the common features successfully indicates the reproducibility of each experiment prior to MS/MS peptide sequencing in three different quantitation strategies: decoupled, coupled isotope-coded affinity tag, and coupled stable isotope labeling of amino acids in cell culture experiments.

Journal: Molecular & Cellular Proteomics: MCP, Aug. 1
Title: Performance characteristics of electron transfer dissociation mass spectrometry
Authors: DM Good; M Wirtala; GC McAlister; JJ Coon
Authors performed a large-scale study of electron transfer dissociation performance and compared the results to ion trap collision-activated dissociation for peptides ranging from about 1,000 Daltons to 5,000 Daltons. They report that ETD outperformed CAD for all charge states greater than two though a linear decrease in percent fragmentation was observed with ETD fragmentation.

Journal: Nature Reviews, Molecular Cell Biology, August
Title: Analysis of protein complexes using mass spectrometry
Authors: AC Gingras; M Gstaiger; B Raught; R Aebersold
Affinity purification and mass spectrometry has been applied to the detailed characterization of many protein complexes and large protein-interaction networks, the authors said in the abstract. Combining AP-MS with other techniques such as biochemical fractionation and intact mass measurement can help to decipher the supramolecular organization of protein complexes, and combined with quantitative proteomics approaches can lead to better understanding of the dynamics of protein-complex assembly.

Journal: Proteomics, August
Title: High performance proteomics: 7th HUPO Brain Proteome Project workshop March 7-9, 2007 Wellcome Trust Conference Center, Hinxton, UK
Authors: M Hamacher; C Stephan; M Eisenacher; P Lewczuk; J Wiltfang; L Martens; JA VizcaÍno; KH Kwon; JS Yoo; YM Park; J Beckers; M Horsch; MH de Angelis; ZH Cho; R Apweiler; HE Meyer
Authors report on the High Performance Proteomics workshop. “The presentation and accompanying vivid discussions created a picture of actual strategies and standards in recent proteomics,” according to the abstract.

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