New Journal Summaries Posted - Tue, Oct 7, 0:49 PM
Submitted By: Mark Gjukich
New Journal Summaries posted. Check out our ,a href="http://www.proteomecommons.org/news/journals.jsp">Journal Summaries page for the latest contents of several popular journals.
Version 2 of the NIST Peptide Mass Spectral Libraries - Mon, Sep 15, 3:29 PM
Submitted By: Mark Gjukich
NIST Mass Spectrometry Data Center:
We are happy to announce that version 2 of our libraries are available for download both on the PeptideAtlas site (http://www.peptideatlas.org/speclib/) and on our newly launched website (http://peptide.nist.gov). Growth of the libraries is presented here (http://peptide.nist.gov/docs/growth2008.pdf). These libraries are meant to demonstrate the utility of peptide ion fragmentation libraries by enabling the development of software applications that use them for identifying peptides by mass spectrometry. While some of the libraries are built from a limited few datasets, others (e.g. yeast, e. coli and human) are large enough for general use. The NIST website also contains additional background information, including reprints and slides from recent presentations. We have also added a spectral library browser to the site, which enables queries of the libraries' content; for example, the browser can be used to view the coverage of a target protein in the library and extract a list of observed peptides according to their observed frequencies. If you wish to use SpectraST (ISB) to search these libraries, you will first need to convert the .msp files to SpectraST format or download the pre-formatted versions from the PeptideAtlas site. Full user information for SpectraST can be found here (http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST). By the end of the year, we hope to release an updated version of our MS Search Software for peptides as well as a new programmer's dll with demonstration code. Lastly, the utility of these community-based libraries greatly improves with public data donations. Your data will be included in the consensus building steps of the next versions of the libraries. Data need only be minimally annotated and donations can be made anonymous.
X!!Tandem now available - Fri, Aug 15, 10:21 AM
Submitted By: Mark Gjukich
Announcing the availability of X!!Tandem, a version of X!Tandem parallelized for running on clusters or networks of workstations. X!!Tandem is a parallel, high performance version of X!Tandem that has been parallelized via MPI to run efficiently on large numbers of CPUs. In X!!Tandem the search is parallelized by splitting the input spectra into as many subsets as there are processors, and processing each subset independently. Both compute-intensive stages of the processing (initial and refinement) are parallelized, and overall speedups in excess of 20-fold have been observed on real datasets. With the exception of minor details related to MPI's program launching, X!!Tandem is run in exactly the same manner as X!Tandem, using the same input and configuration files, and produces exactly the same output. X!!Tandem is a project of Yale's Keck Biotechnology Resource Laboratory, and was developed by Robert Bjornson (robert.bjornson@yale.edu). The package can be downloaded from here.
New journal updates for August on our Journals Summaries page - Fri, Aug 1, 10:41 AM
Submitted By: Mark Gjukich
New Journal Summaries posted. Check out our ,a href="http://www.proteomecommons.org/news/journals.jsp">Journal Summaries page for the latest contents of several popular journals.
New journal updates for July on our Journals Summaries page - Wed, Jul 9, 11:31 AM
Submitted By: Mark Gjukich
New Journal Summaries posted. Check out our Journal Summaries page for the latest contents of several popular journals.
Product review of LIMS use in MS proteomics - Tue, Jul 1, 2:48 PM
Submitted By: Mark Gjukich
Reviews of basic LIMS in related use for MS laboratories and proteomics research. Several systems investigated and broken down into various comparison tables.
PSI MIAPE: Column Chromatography Documentation - Fri, Jun 13, 2:11 PM
Submitted By: Mark Gjukich
PSI MIAPE: Column Chromatography Documentation is available for download here.
PSI mzML 1.0.0 Specification - Fri, Jun 13, 2:04 PM
Submitted By: Mark Gjukich
From 2005-2008 there has existed two separate XML formats for encoding raw spectrometer output: mzData developed by the PSI and mzXML developed at the Seattle Proteome Center at the Institute for Systems Biology. It was recognized that the existence of two separate formats for essentially the same thing generated confusion and required extra programming effort. Therefore the PSI, with full participation by ISB, has developed a new format by taking the best aspects of each of the precursor formats to form a single one. It is intended to replace the previous two formats. This new format was originally given a working name of dataXML. The final name is mzML.
As of 2008-06-01, mzML 1.0.0 is ready. Below are the available documents and initial implementations. We encourage the community to begin implementing mzML 1.0.0, to phase out use of mzData and mzXML, and to send feedback to psidev-ms-dev@lists.sourceforge.net.
You can download the mzML: Mass Spectrometer Markup Language Specification document here
Newest Journal Summaries Now Available - Mon, Jun 2, 4:00 PM
Submitted By: Mark Gjukich
New journal summaries posted. Check out our Journal Summaries page for the latest contents of several popular journals.
New Cross-Platform Proteomics Tool Available - Thu, May 22, 4:06 PM
Submitted By: Mark Gjukich
A new cross-platform proteomics tool is now available from the Cedar-Sinai Spielberg Family Center for Applied Proteomics.
ProteoWizard is a modular and extensible set of open-source, cross-platform tools and software libraries for proteomics data analysis.
The libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.
The software is available for download now, under the Apache open source license.
You can find more about this and many other proteomics tools on our the ProteomeCommons.org Tools page.
SPS' Digest Issue 51, 16-May-2008 - Wed, May 21, 11:18 AM
Submitted By: Mark Gjukich
The 51th Issue of SPS' Digest is now available at: http://www.swissproteomicsociety.org/digest/2008/issue51.html
It contains the SPS selection of proteomics articles gathered from the scientific literature during the month, currently 356 articles in 130 journals (Anal Bioanal Chem, Analytical Biochemistry, Analytical Chemistry, BMB Rep, Bioinformatics, Contrib Nephrol, Curr Protoc Bioinformatics, Curr Protoc Protein Sci, Electrophoresis, Expert Rev Proteomics, J Proteome Res, Journal of Proteomics, Mar Environ Res, Mass Spectrom Rev, Methods Enzymol, Methods Mol Biol, Mol Cell Proteomics, Nucl Acids Res, PLoS ONE, Proteomics, etc.).
50,000,000th Peptide Id Recorded - Wed, May 21, 10:49 AM
Submitted By: Mark Gjukich
The GPMDB passed the 50 million mark for peptide identifications. For more information, please visit the GPM website at www.thegpm.org
New TPP Release: Version 3.5.4 - Mon, May 12, 10:30 AM
Submitted By: Mark Gjukich
The Trans-Proteomic Pipeline 3.5.x series has been updated with the release of version 3.5.4 (cygwin package ISB-MS-Tools-3.5-4a). All 3.5.x users are encouraged to update.
http://tools.proteomecenter.org/TPP.php
TPP Version 3.5.4 changes (since 3.5.3)
IMPORTANT NOTE: converter binaries are not distributed in this version. Please download them directly from SourceForge (see links below). Please remember, you must run the vcredist_x86.exe program one time, before running the converters.
New ProteinProphet options
New command-line options: PROTLEN (calculates protein length and reports it in protXML), NORMPROTLEN (normalizes NSP by protein length; previously PROTLEN param), PROTMW (calculates protein molecular weight from the database and reports it in protXML).
Temp Files
Improved handling for temporary files throughout the TPP
Mascot2XML
Another fix to Mascot2XML to handle "Scan Number: nnn" variant of scan title, appearing in some Mascot files.
Converters(ReAdW, wolf, mzWiff)
* Minor bug fixed in experimental mzML output: base peak m/z and intensity values had been reversed.
For downloading and installing the Windows version please visit the
following guide on our wiki:
http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation
For downloading the source code, please go to the following link:
http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912
or directly from svn:
http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_3-5-4
Please refer to the readme file in TPP/src as well as the wiki.
Bioinformatics: Volume 24, Number 10, 8 May 2008 - Thu, May 8, 10:40 AM
Submitted By: Mark Gjukich
Latest contents of Oxford Journals, Bioinformatics now available online. You may have to have a subscription to read the on-line articles.
Bioinformatics: Volume 23, Number 22, 15 November 2007 - Tue, Nov 20, 10:36 PM
Submitted By: Jayson A. Falkner
A new issue of Bioinformatics is now available. Here is a summary of the original papers. Links are provided to the on-line HTML and PDF files for the research articles. You may have to have a subscription to read the on-line articles.
- Evolutionary analysis of enzymes using Chisel
[Abstract], [Full Text], [Print PDF]
Alexis A. Rodriguez, Tanuja Bompada, Mustafa Syed, Parantu K. Shah, and Natalia Maltsev - Multiple spaced seeds for homology search
[Abstract], [Full Text], [Print PDF]
Lucian Ilie and Silvana Ilie - Annotation of selection strengths in viral genomes
[Abstract], [Full Text], [Print PDF]
Stephen McCauley, Saskia de Groot, Thomas Mailund, and Jotun Hein - Naïve Bayes for microRNA target predictions—machine learning for microRNA targets
[Abstract], [FREE Full Text], [Print PDF]
Malik Yousef, Segun Jung, Andrew V. Kossenkov, Louise C. Showe, and Michael K. Showe - Sliding MinPD: building evolutionary networks of serial samples via an automated recombination detection approach
[Abstract], [Full Text], [Print PDF]
Patricia Buendia and Giri Narasimhan - The Poisson Index: a new probabilistic model for protein–ligand binding site similarity
[Abstract], [Full Text], [Print PDF]
J.R. Davies, R.M. Jackson, K.V. Mardia, and C.C. Taylor - Four-Body Scoring Function for Mutagenesis
[Abstract], [Full Text], [Print PDF]
Chris Deutsch and Bala Krishnamoorthy - PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra
[Abstract], [Full Text], [Print PDF]
Franz F. Roos, Riko Jacob, Jonas Grossmann, Bernd Fischer, Joachim M. Buhmann, Wilhelm Gruissem, Sacha Baginsky, and Peter Widmayer - Improved detection of overrepresentation of Gene-Ontology annotations with parent–child analysis
[Abstract], [FREE Full Text], [Print PDF]
Steffen Grossmann, Sebastian Bauer, Peter N. Robinson, and Martin Vingron - The high-level similarity of some disparate gene expression measures
[Abstract], [Full Text], [Print PDF]
Nandini Raghavan, An M. I. M. De Bondt, Willem Talloen, Dieder Moechars, Hinrich W. H. Göhlmann, and Dhammika Amaratunga - Context-dependent clustering for dynamic cellular state modeling of microarray gene expression
[Abstract], [Full Text], [Print PDF]
Shinsheng Yuan and Ker-Chau Li - HAPLOPOOL: improving haplotype frequency estimation through DNA pools and phylogenetic modeling
[Abstract], [Full Text], [Print PDF]
Bonnie Kirkpatrick, Carlos Santos Armendariz, Richard M. Karp, and Eran Halperin - Inferring transcriptional regulatory networks from high-throughput data
[Abstract], [Full Text], [Print PDF]
Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, and Luonan Chen - Intersession reproducibility of mass spectrometry profiles and its effect on accuracy of multivariate classification models
[Abstract], [Full Text], [Print PDF]
Richard Pelikan, William L. Bigbee, David Malehorn, James Lyons-Weiler, and Milos Hauskrecht - Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics
[Abstract], [FREE Full Text], [Print PDF]
Andrew Smith, Kei Cheung, Michael Krauthammer, Martin Schultz, and Mark Gerstein - A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data
[Abstract], [FREE Full Text], [Print PDF]
Lennart J. G. Post, Marco Roos, M. Scott Marshall, Roel van Driel, and Timo M. Breit - CONSORF: a consensus prediction system for prokaryotic coding sequences
[Abstract], [FREE Full Text], [Print PDF]
Sungsoo Kang, Sung-Jin Yang, Sangsoo Kim, and Jong Bhak - Genomic mutation consequence calculator
[Abstract], [FREE Full Text], [Print PDF]
John E. Major - BiasViz: visualization of amino acid biased regions in protein alignments
[Abstract], [FREE Full Text], [Print PDF]
Matthew R. Huska, Henrik Buschmann, and Miguel A. Andrade-Navarro - HMM-Kalign: a tool for generating sub-optimal HMM alignments
[Abstract], [Full Text], [Print PDF]
Emmanuelle Becker, Aurélie Cotillard, Vincent Meyer, Hocine Madaoui, and Raphaël Guérois - Functional profiling of microarray experiments using text-mining derived bioentities
[Abstract], [FREE Full Text], [Print PDF]
Pablo Minguez, Fátima Al-Shahrour, David Montaner, and Joaquín Dopazo - TAPPA: topological analysis of pathway phenotype association
[Abstract], [Full Text], [Print PDF]
Shouguo Gao and Xujing Wang - CellMontage: similar expression profile search server
[Abstract], [Full Text], [Print PDF]
Wataru Fujibuchi, Larisa Kiseleva, Takeaki Taniguchi, Hajime Harada, and Paul Horton - IGG: A tool to integrate GeneChips for genetic studies
[Abstract], [Full Text], [Print PDF]
M.-X. Li, L. Jiang, S.-L. Ho, Y.-Q. Song, and P.-C. Sham - Marker development for the genetic study of natural variation in Arabidopsis thaliana
[Abstract], [Full Text], [Print PDF]
Adnane Nemri, Michael M. Neff, Michael Burrell, Jonathan D.G. Jones, and David J. Studholme - MeTaDoR: a comprehensive resource for membrane targeting domains and their host proteins
[Abstract], [Full Text], [Print PDF]
Nitin Bhardwaj, Robert V. Stahelin, Guijun Zhao, Wonhwa Cho, and Hui Lu
Bioinformatics: Volume 23, Number 20, 15 October 2007 - Sun, Nov 4, 1:06 AM
Submitted By: Jayson A. Falkner
A new issue of Bioinformatics is now available. Here is a summary of the original papers. Links are provided to the on-line HTML and PDF files for the research articles. You may have to have a subscription to read the on-line articles.
- Tools for visually exploring biological networks
[Abstract], [Full Text], [Print PDF]
Matthew Suderman and Michael Hallett - The DOMON domains are involved in heme and sugar recognition
[Abstract], [Full Text], [Print PDF]
Lakshminarayan M. Iyer, Vivek Anantharaman, and L. Aravind - Effect of the mutation rate and background size on the quality of pathogen identification
[Abstract], [Full Text], [Print PDF]
Chris Reed, Viacheslav Fofanov, Catherine Putonti, Sergei Chumakov, Tom Slezak, and Yuriy Fofanov - Identification of compositionally distinct regions in genomes using the centroid method
[Abstract], [Full Text], [Print PDF]
Issaac Rajan, Sarang Aravamuthan, and Sharmila S. Mande - Structure-based calculation of drug efficiency indices
[Abstract], [FREE Full Text], [Print PDF]
Csaba Hetényi, Uko Maran, Alfonso T. García-Sosa, and Mati Karelson - Expression ratio evaluation in two-colour microarray experiments is significantly improved by correcting image misalignment
[Abstract], [Full Text], [Print PDF]
Thomas Tang, Nicolas François, Annie Glatigny, Nicolas Agier, Marie-Hélène Mucchielli, Lawrence Aggerbeck, and Hervé Delacroix - Exploring the functional landscape of gene expression: directed search of large microarray compendia
[Abstract], [Full Text], [Print PDF]
Matthew A. Hibbs, David C. Hess, Chad L. Myers, Curtis Huttenhower, Kai Li, and Olga G. Troyanskaya - A comparison of background correction methods for two-colour microarrays
[Abstract], [Full Text], [Print PDF]
Matthew E. Ritchie, Jeremy Silver, Alicia Oshlack, Melissa Holmes, Dileepa Diyagama, Andrew Holloway, and Gordon K. Smyth - Clustering by soft-constraint affinity propagation: applications to gene-expression data
[Abstract], [Full Text], [Print PDF]
Michele Leone, Sumedha, and Martin Weigt - Construction of a reference gene association network from multiple profiling data: application to data analysis
[Abstract], [Full Text], [Print PDF]
Duygu Ucar, Isaac Neuhaus, Petra Ross-MacDonald, Charles Tilford, Srinivasan Parthasarathy, Nathan Siemers, and Rui-Ru Ji - Fun&Co: identification of key functional differences in transcriptomes
[Abstract], [Full Text], [Print PDF]
Giacomo Gamberoni, Evelina Lamma, Gianluca Lodo, Jlenia Marchesini, Nicoletta Mascellani, Simona Rossi, Sergio Storari, Luca Tagliavini, and Stefano Volinia - Exploiting sample variability to enhance multivariate analysis of microarray data
[Abstract], [Full Text], [Print PDF]
Carla S. Möller-Levet, Catharine M. West, and Crispin J. Miller - A genotype calling algorithm for the Illumina BeadArray platform
[Abstract], [Full Text], [Print PDF]
Yik Y. Teo, Michael Inouye, Kerrin S. Small, Rhian Gwilliam, Panagiotis Deloukas, Dominic P. Kwiatkowski, and Taane G. Clark - An error model for protein quantification
[Abstract], [Full Text], [Print PDF]
C. Kreutz, M.M. Bartolome Rodriguez, T. Maiwald, M. Seidl, H.E. Blum, L. Mohr, and J. Timmer - Metal reduction kinetics in Shewanella
[Abstract], [Full Text], [Print PDF]
Raman Lall and Julie Mitchell - A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts
[Abstract], [Full Text], [Print PDF]
Yizhi Cai, Brian Hartnett, Claes Gustafsson, and Jean Peccoud - Learning string similarity measures for gene/protein name dictionary look-up using logistic regression
[Abstract], [Full Text], [Print PDF]
Yoshimasa Tsuruoka, John McNaught, Jun'i;chi Tsujii, and Sophia Ananiadou - Mining biological networks for unknown pathways
[Abstract], [Full Text], [Print PDF]
Ali Cakmak and Gultekin Ozsoyoglu - MSQT for choosing SNP assays from multiple DNA alignments
[Abstract], [Full Text], [Print PDF]
Norman Warthmann, Joffrey Fitz, and Detlef Weigel - A parsimonious threshold-independent protein feature selection method through the area under receiver operating characteristic curve
[Abstract], [Full Text], [Print PDF]
Zhanfeng Wang, Yuan-chin I. Chang, Zhiliang Ying, Liang Zhu, and Yaning Yang - TMpro web server and web service: transmembrane helix prediction through amino acid property analysis
[Abstract], [Full Text], [Print PDF]
Madhavi Ganapathiraju, Christopher Jon Jursa, Hassan A. Karimi, and Judith Klein-Seetharaman - Identification of potential HIV-1 targets of minocycline
[Abstract], [Full Text], [Print PDF]
Ekachai Jenwitheesuk and Ram Samudrala - Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes
[Abstract], [Full Text], [Print PDF]
Sean Sedwards and Tommaso Mazza - AVIS: AJAX viewer of interactive signaling networks
[Abstract], [Full Text], [Print PDF]
Seth I. Berger, Ravi Iyengar, and Avi Ma’ayan
Journal of Proteome Research: Vol. 6, No. 11: November 2007 - Sun, Nov 4, 1:05 AM
Submitted By: Jayson A. Falkner
- COMET and the Challenge of Drug Safety Screening (
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Jeremy Nicholson, Hector Keun, and Tim Ebbels
- Currents: A bead-based kinase competition assay for chemical proteomics | Calcium phosphate precipitation and IMAC for phosphopeptide enrichment | A new protein PTM: pyrophosphorylation | Proteomics with a PVDF membrane | Microfluidic 2D DIGE analyzer | Metabonomics for toxicity monitoring (
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pp 4101 - 4103 - TOOLbox: NetworKIN | myProMS | Chaorder assesses experimental bias | Glycan analysis (
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pp 4102 - 4103
- Research Profile: Who really needs a cervical biopsy? (
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Katie Cottingham - Research Profile: A molecular picture of chocoholics (
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Jeffrey M. Perkel - Research Profile: Proteome changes in HIV-associated dementia (
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Laura Cassiday - Proteomics Projects: HuPI focuses on protein interactions (
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Katie Cottingham - Government & Society: CIHR requires open access (
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p 4107
PRODUCT NOTES
- New Products (
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p 4109
- Proteomic Analysis Reveals Differences in Protein Expression in Spheroid versus Monolayer Cultures of Low-Passage Colon Carcinoma Cells (
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Lars Gaedtke, Lilja Thoenes, Carsten Culmsee, Barbara Mayer, and Ernst Wagner - A Strategic Fluorescence Labeling of D-Galactose/D-Glucose-Binding Protein from Escherichia coli Helps to Shed Light on the Protein Structural Stability and Dynamics (
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, Viviana Scognamiglio, Andrea Scirè, Vincenzo Aurilia, Maria Staiano, Roberta Crescenzo, Cristina Palmucci, Enrico Bertoli, Mosè Rossi, Fabio Tanfani, and Sabato D'Auria
- Specific MALDI Imaging and Profiling for Biomarker Hunting and Validation: Fragment of the 11S Proteasome Activator Complex, Reg Alpha Fragment, Is a New Potential Ovary Cancer Biomarker (
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, Remi Lemaire, Sonia Ait Menguellet, Jonathan Stauber, Valerie Marchaudon, Jean-Philippe Lucot, Pierre Collinet, Marie-Odile Farine, Denis Vinatier, Robert Day, Patrick Ducoroy, Michel Salzet, and Isabelle Fournier
- Application of Fluorescence Difference Gel Electrophoresis Technology in Searching for Protein Biomarkers in Chick Myopia (
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, Thomas C. Lam, King-Kit Li, Samuel C. L. Lo, Jeremy A. Guggenheim, and Chi Ho To
- Improved Titanium Dioxide Enrichment of Phosphopeptides from HeLa Cells and High Confident Phosphopeptide Identification by Cross-Validation of MS/MS and MS/MS/MS Spectra (
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, Li-Rong Yu, Zhongyu Zhu, King C. Chan, Haleem J. Issaq, Dimiter S. Dimitrov, and Timothy D. Veenstra
- Proteome Changes Induced by Knock-Down of the Deubiquitylating Enzyme HAUSP/USP7 (
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, Benedikt M. Kessler, Elisabetta Fortunati, Monique Melis, Cornelieke E.G.M. Pals, Hans Clevers, and Madelon M. Maurice
- Bacterial Overgrowth Affects Urinary Proteome Analysis: Recommendation for Centrifugation, Temperature, Duration, and the Use of Preservatives during Sample Collection (
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, Visith Thongboonkerd and Putita Saetun
- The Tumor Suppressors p33ING1 and p33ING2 Interact with Alien in Vivo and Enhance Alien-Mediated Gene Silencing (
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Inga Fegers, Robert Kob, Maren Eckey, Oliver Schmidt, Frauke Goeman, Maria Papaioannou, Niko Escher, Ferdinand von Eggeling, Christian Melle, and Aria Baniahmad - Cerebrospinal Fluid Proteomic Profiling of HIV-1-Infected Patients with Cognitive Impairment (
Wojciech Rozek, Mary Ricardo-Dukelow, Sondra Holloway, Howard E. Gendelman, Valerie Wojna, Loyda M. Melendez, and Pawel Ciborowski
- iTRAQ Reagent-Based Quantitative Proteomic Analysis on a Linear Ion Trap Mass Spectrometer (
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, Timothy J. Griffin, Hongwei Xie, Sricharan Bandhakavi, Jonathan Popko, Archana Mohan, John V. Carlis, and LeeAnn Higgins
- Experimental Approach for Assessing the Outcome Accuracy of Antibody Microarray Experiments (
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, Qiang Gu, Thamil Mani Sivanandam, and Jessica Haymore
- Development of a Highly Sensitive, High-Throughput, Mass Spectrometry-Based Assay for Rat Procollagen Type-I N-Terminal Propeptide (PINP) To Measure Bone Formation Activity (
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, Bomie Han, Marci Copeland, Andrew G. Geiser, Laura V. Hale, Anita Harvey, Yanfei L. Ma, Connie S. Powers, Masahiko Sato, Jinsam You, and John E. Hale
- On-Line LC-MS Approach Combining Collision-Induced Dissociation (CID), Electron-Transfer Dissociation (ETD), and CID of an Isolated Charge-Reduced Species for the Trace-Level Characterization of Proteins with Post-Translational Modifications (
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, Shiaw-Lin Wu, Andreas F. R. Hühmer, Zhiqi Hao, and Barry L. Karger
- Essential Dynamics of Helices Provide a Functional Classification of EF-Hand Proteins (
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, Francesco Capozzi, Claudio Luchinat, Cristian Micheletti, and Francesco Pontiggia
- Proteomic Analysis of High-Grade Dysplastic Cervical Cells Obtained from ThinPrep Slides Using Laser Capture Microdissection and Mass Spectrometry (
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, Ye Gu, Shiaw-Lin Wu, Jane L. Meyer, William S. Hancock, Lawrence J. Burg, James Linder, David W. Hanlon, and Barry L. Karger
- Cyanogen Bromide Peptides of the Fibrillar Collagens I, III, and V and Their Mass Spectrometric Characterization: Detection of Linear Peptides, Peptide Glycosylation, and Cross-Linking Peptides Involved in Formation of Homo- and Heterotypic Fibrils (
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, Werner Henkel and Klaus Dreisewerd
- Exploring the Platelet Proteome via Combinatorial, Hexapeptide Ligand Libraries (
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, Luc Guerrier, Stephane Claverol, Frederic Fortis, Sara Rinalducci, Anna Maria Timperio, Paolo Antonioli, Martine Jandrot-Perrus, Egisto Boschetti, and Pier Giorgio Righetti
- A New Approach for Mapping Sialylated N-Glycosites in Serum Proteomes (
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, Bart Ghesquière, Lien Buyl, Hans Demol, Jozef Van Damme, An Staes, Evy Timmerman, Joël Vandekerckhove, and Kris Gevaert
- Mass Spectral Compatibility of Four Proteomics Stains (
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, Malcolm S. Ball and Peter Karuso
- Proteomic Approach for Caudal Trauma-Induced Acute Phase Proteins Reveals That Creatine Kinase Is a Key Acute Phase Protein in Amphioxus Humoral Fluid (
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, Yuan-yuan Gao, Dan-feng Zhang, Hui Li, Runzhong Liu, Zheng-hong Zhuang, Qi-fu Li, San-ying Wang, and Xuan-xian Peng
- Comparative Proteome Profiling and Functional Analysis of Chronic Myelogenous Leukemia Cell Lines (
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, Simona Fontana, Riccardo Alessandro, Marilisa Barranca, Margherita Giordano, Chiara Corrado, Isabelle Zanella-Cleon, Michel Becchi, Elise C. Kohn, and Giacomo De Leo
- Proteomic Identification of the Cerebral Cavernous Malformation Signaling Complex (
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, Thomas L. Hilder, Michael H. Malone, Sompop Bencharit, John Colicelli, Timothy A. Haystead, Gary L. Johnson, and Christine C. Wu
- Proteomic Analysis of Peritoneal Dialysate Fluid in Patients with Different Types of Peritoneal Membranes (
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, Suchai Sritippayawan, Wararat Chiangjong, Theptida Semangoen, Nipa Aiyasanon, Parnthip Jaetanawanitch, Supachok Sinchaikul, Shui-Tein Chen, Somkiat Vasuvattakul, and Visith Thongboonkerd
- Two-Dimensional Reversed-Phase × Ion-Pair Reversed-Phase HPLC: An Alternative Approach to High-Resolution Peptide Separation for Shotgun Proteome Analysis (
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, Nathanaël Delmotte, Maria Lasaosa, Andreas Tholey, Elmar Heinzle, and Christian G. Huber
- Glycomics of Proteoglycan Biosynthesis in Murine Embryonic Stem Cell Differentiation (
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, Alison V. Nairn, Akiko Kinoshita-Toyoda, Hidenao Toyoda, Jin Xie, Kyle Harris, Stephen Dalton, Michael Kulik, J. Michael Pierce, Toshihiko Toida, Kelley W. Moremen, and Robert J. Linhardt
- Profiling of Endogenous Peptides in Human Synovial Fluid by NanoLC-MS: Method Validation and Peptide Identification (
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, Jurre J. Kamphorst, Rob van der Heijden, Jeroen DeGroot, Floris P. J. G. Lafeber, Theo H. Reijmers, Benno van El, Ubbo R. Tjaden, Jan van der Greef, and Thomas Hankemeier
- Identification of Ubiquitin Target Proteins Using Cell-Based Arrays (
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, Tao Zhou, Bing Liang, Gui-Ying Su, Wei-Li Gong, Hui-Yan Li, Li-Feng Tian, Kun He, Jie Zhao, Jiang-Hong Man, Tao Li, Wei-Hua Li, Zhi-Yi Zhang, Chen-Hui Wang, Ai-Ling Li, Hui Liu, Xin Pan, Pei-Jing Zhang, Bao-Feng Jin, and Xue-Min Zhang
- Prediction and Classification of Drug Toxicity Using Probabilistic Modeling of Temporal Metabolic Data: The Consortium on Metabonomic Toxicology Screening Approach (
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, Timothy M. D. Ebbels, Hector C. Keun, Olaf P. Beckonert, Mary E. Bollard, John C. Lindon, Elaine Holmes, and Jeremy K. Nicholson
- Comparative Analysis of the Protein Profiles from Primary Gastric Tumors and Their Adjacent Regions: MAWBP Could Be a New Protein Candidate Involved in Gastric Cancer (
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, Jun Zhang, Bin Kang, Xiaohui Tan, Zhigang Bai, Yumei Liang,O, Rui Xing, Jianmin Shao, Ningzhi Xu, Rong Wang, Siqi Liu, and Youyong Lu
- Characterization of Amyloid
Peptides in Cerebrospinal Fluid by an Automated Immunoprecipitation Procedure Followed by Mass Spectrometry (
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, Erik Portelius, Ai Jun Tran, Ulf Andreasson, Rita Persson, Gunnar Brinkmalm, Henrik Zetterberg, Kaj Blennow, and Ann Westman-Brinkmalm - Searching Urinary Tumor Markers for Bladder Cancer Using a Two-Dimensional Differential Gel Electrophoresis (2D-DIGE) Approach (
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, Esteban Orenes-Piñero, Marta Cortón, Pilar González-Peramato, Ferrán Algaba, Ignacio Casal, Alvaro Serrano, and Marta Sánchez-Carbayo
- Organellar Proteomics of Human Platelet Dense Granules Reveals That 14-3-3
Is a Granule Protein Related to Atherosclerosis (
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, Laura Hernández-Ruiz, Federico Valverde, Maria D. Jimenez-Nuñez, Esther Ocaña, Ana Sáez-Benito, Javier Rodríguez-Martorell, Juan-Carlos Bohórquez, Aurelio Serrano, and Felix A. Ruiz - "Turnover Proteome" of Human Atrial Trabeculae (
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, Florian M. Lampert, Peter Matt, Martin Grapow, Ivan Lefkovits, Hans-Reinhard Zerkowski, and Thomas Grussenmeyer
- Human Metabolic Phenotypes Link Directly to Specific Dietary Preferences in Healthy Individuals (
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, Serge Rezzi, Ziad Ramadan, François-Pierre J. Martin, Laurent B. Fay, Peter van Bladeren, John C. Lindon, Jeremy K. Nicholson, and Sunil Kochhar
- Proteomic Identification of PKC-Mediated Expression of 20E-Induced Protein in Drosophila melanogaster (
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Yaning Sun, Shiheng An, Vincent C. Henrich, Xiaoping Sun, and Qisheng Song
- Applying a Targeted Label-Free Approach Using LC-MS AMT Tags to Evaluate Changes in Protein Phosphorylation Following Phosphatase Inhibition (
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, Feng Yang, Navdeep Jaitly, Hemalatha Jayachandran, Quanzhou Luo, Matthew E. Monroe, Xiuxia Du, Marina A. Gritsenko, Rui Zhang, David J. Anderson, Samuel O. Purvine, Joshua N. Adkins, Ronald J. Moore, Heather M. Mottaz, Shi-Jian Ding, Mary S. Lipton, David G. Camp, II, Harold R. Udseth, Richard D. Smith, and Sandra Rossie
- Preparation of Fe3O4@ZrO2 Core-Shell Microspheres as Affinity Probes for Selective Enrichment and Direct Determination of Phosphopeptides Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (
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, Yan Li, Taohua Leng, Huaqing Lin, Chunhui Deng, Xiuqing Xu, Ning Yao, Pengyuan Yang, and Xiangmin Zhang
- Differential Recovery of Peptides from Sample Tubes and the Reproducibility of Quantitative Proteomic Data (
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, Steven J. Bark and Vivian Hook
- Optimization of MALDI-TOF MS Detection for Enhanced Sensitivity of Affinity-Captured Proteins Spanning a 100 kDa Mass Range (
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, Christine L. Gatlin-Bunai, Lisa H. Cazares, William E. Cooke, Oliver J. Semmes, and Dariya I. Malyarenko
- Integration of Residue-Specific Acid Cleavage into Proteomic Workflows (
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Steven Swatkoski, Peter Gutierrez, Joy Ginter, Alexey Petrov, Jonathan D. Dinman, Nathan Edwards, and Catherine Fenselau
- Method Development of Efficient Protein Extraction in Bone Tissue for Proteome Analysis J. Proteome Res. 2007, 6, 2287-2294. (
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Xiaogang Jiang, Mingliang Ye, Xinning Jiang, Guangpeng Liu, Shun Feng, Lei Cui,and, and Hanfa Zou
Bioinformatics: Volume 23, Number 18, 15 September 2007 - Wed, Oct 24, 6:22 AM
Submitted By: Jayson A. Falkner
A new issue of Bioinformatics is now available. Here is a summary of the original papers. Links are provided to the on-line HTML and PDF files for the research articles. You may have to have a subscription to read the on-line articles.
- Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone
[Abstract], [Full Text], [Print PDF]
Adam James Reid, Corin Yeats, and Christine Anne Orengo - The global trace graph, a novel paradigm for searching protein sequence databases
[Abstract], [FREE Full Text], [Print PDF]
Andreas Heger, Swapan Mallick, Christopher Wilton, and Liisa Holm - A quantitative genotype algorithm reflecting H5N1 Avian influenza niches
[Abstract], [FREE Full Text], [Print PDF]
Xiu-Feng Wan, Guorong Chen, Feng Luo, Michael Emch, and Ruben Donis - Natively unstructured regions in proteins identified from contact predictions
[Abstract], [FREE Full Text], [Print PDF]
Avner Schlessinger, Marco Punta, and Burkhard Rost - AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets
[Abstract], [FREE Full Text], [Print PDF]
Hongfang Liu, Barry R. Zeeberg, Gang Qu, A. Gunes Koru, Alessandro Ferrucci, Ari Kahn, Michael C. Ryan, Antej Nuhanovic, Peter J. Munson, William C. Reinhold, David W. Kane, and John N. Weinstein - Selection and validation of normalization methods for c-DNA microarrays using within-array replications
[Abstract], [Full Text], [Print PDF]
Jianqing Fan and Yue Niu - Haplotype inference for present–absent genotype data using previously identified haplotypes and haplotype patterns
[Abstract], [Full Text], [Print PDF]
Yun Joo Yoo, Jianming Tang, Richard A. Kaslow, and Kui Zhang - LICORN: learning cooperative regulation networks from gene expression data
[Abstract], [Full Text], [Print PDF]
Mohamed Elati, Pierre Neuvial, Monique Bolotin-Fukuhara, Emmanuel Barillot, François Radvanyi, and Céline Rouveirol - Robustness analysis and tuning of synthetic gene networks
[Abstract], [Full Text], [Print PDF]
Grégory Batt, Boyan Yordanov, Ron Weiss, and Calin Belta - miniTUBA: medical inference by network integration of temporal data using Bayesian analysis
[Abstract], [Full Text], [Print PDF]
Zuoshuang Xiang, Rebecca M. Minter, Xiaoming Bi, Peter J. Woolf, and Yongqun He - Modular decomposition of metabolic reaction networks based on flux analysis and pathway projection
[Abstract], [Full Text], [Print PDF]
Jeongah Yoon, Yaguang Si, Ryan Nolan, and Kyongbum Lee - Quantitative quality-assessment techniques to compare fractionation and depletion methods in SELDI-TOF mass spectrometry experiments
[Abstract], [Full Text], [Print PDF]
Jaroslaw Harezlak, Mike Wang, David Christiani, and Xihong Lin - An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization
[Abstract], [Full Text], [Print PDF]
Ziliang Qian, Lingyi Lu, XiaoJun Liu, Yu-Dong Cai, and Yixue Li - Mining complex genotypic features for predicting HIV-1 drug resistance
[Abstract], [Full Text], [Print PDF]
Hiroto Saigo, Takeaki Uno, and Koji Tsuda - Robust smooth segmentation approach for array CGH data analysis
[Abstract], [Full Text], [Print PDF]
Jian Huang, Arief Gusnanto, Kathleen O'Sullivan, Johan Staaf, Åke Borg, and Yudi Pawitan - Analysis of array CGH data for cancer studies using fused quantile regression
[Abstract], [Full Text], [Print PDF]
Youjuan Li and Ji Zhu - Medline search engine for finding genetic markers with biological significance
[Abstract], [FREE Full Text], [Print PDF]
Weijian Xuan, Pinglang Wang, Stanley J. Watson, and Fan Meng - HMMoC—a compiler for hidden Markov models
[Abstract], [Full Text], [Print PDF]
Gerton Lunter - Quality estimation of multiple sequence alignments by Bayesian hypothesis testing
[Abstract], [FREE Full Text], [Print PDF]
Andrija Tomovic and Edward J. Oakeley - Con-Struct Map: a comparative contact map analysis tool
[Abstract], [FREE Full Text], [Print PDF]
Jo-Lan Chung, John E. Beaver, Eric D. Scheeff, and Philip E. Bourne - RefPlus: an R package extending the RMA Algorithm
[Abstract], [Full Text], [Print PDF]
Chris Harbron, Kai-Ming Chang, and Marie C. South - APID2NET: unified interactome graphic analyzer
[Abstract], [FREE Full Text], [Print PDF]
Juan Hernandez-Toro, Carlos Prieto, and Javier De Las Rivas - sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets
[Abstract], [FREE Full Text], [Print PDF]
Supawadee Ingsriswang and Eakasit Pacharawongsakda - EcoProDB: the Escherichia coli protein database
[Abstract], [Full Text], [Print PDF]
Hongseok Yun, Jeong Wook Lee, Joonwoo Jeong, Jaesung Chung, Jong Myoung Park, Han Na Myoung, and Sang Yup Lee - A Laboratory Information Management System (LIMS) for a high throughput genetic platform aimed at candidate gene mutation screening
[Abstract], [Full Text], [Print PDF]
C. Voegele, S.V. Tavtigian, D. de Silva, S. Cuber, A. Thomas, and F. Le Calvez-Kelm
Molecular and Cellular Proteomics: September 2007, Vol. 6, No. 9 - Sat, Sep 1, 10:07 PM
Submitted By: Jayson A. Falkner
A new issue of Molecular and Cellular Proteomics is now available. Here is a summary of the original papers. Links are provided to the on-line HTML and PDF files for the research articles. You may have to have a subscription to read the on-line articles.
- Salt-induced Changes in the Plasma Membrane Proteome of the Halotolerant Alga Dunaliella salina as Revealed by Blue Native Gel Electrophoresis and Nano-LC-MS/MS Analysis
Adriana Katz, Patrice Waridel, Andrej Shevchenko, and Uri Pick - Protein Sulfenation as a Redox Sensor: Proteomics Studies Using a Novel Biotinylated Dimedone Analogue
Rebecca L. Charles, Ewald Schröder, Georgina May, Paul Free, Piers R. J. Gaffney, Robin Wait, Shajna Begum, Richard J. Heads, and Philip Eaton - Glycomics Analysis of Schistosoma mansoni Egg and Cercarial Secretions
Jihye Jang-Lee, Rachel S. Curwen, Peter D. Ashton, Bérangère Tissot, William Mathieson, Maria Panico, Anne Dell, R. Alan Wilson, and Stuart M. Haslam - In Situ Detection of Phosphorylated Platelet-derived Growth Factor Receptor ß Using a Generalized Proximity Ligation Method
Malin Jarvius, Janna Paulsson, Irene Weibrecht, Karl-Johan Leuchowius, Ann-Catrin Andersson, Carolina Wählby, Mats Gullberg, Johan Botling, Tobias Sjöblom, Boyka Markova, Arne Östman, Ulf Landegren, and Ola Söderberg - Mild Performic Acid Oxidation Enhances Chromatographic and Top Down Mass Spectrometric Analyses of Histones
James J. Pesavento, Benjamin A. Garcia, James A. Streeky, Neil L. Kelleher, and Craig A. Mizzen - Consequences of Membrane Protein Overexpression in Escherichia coli
Samuel Wagner, Louise Baars, A. Jimmy Ytterberg, Anja Klussmeier, Claudia S. Wagner, Olof Nord, Per-Åke Nygren, Klaas J. van Wijk, and Jan-Willem de Gier - Mass Spectrometric Analysis of the Endogenous Type I Interleukin-1 (IL-1) Receptor Signaling Complex Formed after IL-1 Binding Identifies IL-1RAcP, MyD88, and IRAK-4 as the Stable Components
Constantinos Brikos, Robin Wait, Shajna Begum, Luke A. J. O'Neill, and Jeremy Saklatvala - Quantitative Profile of Five Murine Core Proteomes Using Label-free Functional Proteomics
Pedro R. Cutillas and Bart Vanhaesebroeck - Enabling Coupled Quantitative Genomics and Proteomics Analyses from Rat Spinal Cord Samples
R. Hussain Butt, Tom A. Pfeifer, Allen Delaney, Thomas A. Grigliatti, Wolfram G. Tetzlaff, and Jens R. Coorssen - The Implications of Proteolytic Background for Shotgun Proteomics
Paola Picotti, Ruedi Aebersold, and Bruno Domon - Comparative Evaluation of Tandem MS Search Algorithms Using a Target-Decoy Search Strategy
Brian M. Balgley, Tom Laudeman, Li Yang, Tao Song, and Cheng S. Lee - Shotgun Identification of the Structural Proteome of Shrimp White Spot Syndrome Virus and iTRAQ Differentiation of Envelope and Nucleocapsid Subproteomes
Zhengjun Li, Qingsong Lin, Jing Chen, Jin Lu Wu, Teck Kwang Lim, Siew See Loh, Xuhua Tang, and Choy-Leong Hew - Mascot File Parsing and Quantification (MFPaQ), a New Software to Parse, Validate, and Quantify Proteomics Data Generated by ICAT and SILAC Mass Spectrometric Analyses: Application To the Proteomics Study of Membrane Proteins from Primary Human Endothelial Cells
David Bouyssié, Anne Gonzalez de Peredo, Emmanuelle Mouton, Renaud Albigot, Lucie Roussel, Nathalie Ortega, Corinne Cayrol, Odile Burlet-Schiltz, Jean-Philippe Girard, and Bernard Monsarrat - The Paragon Algorithm, a Next Generation Search Engine That Uses Sequence Temperature Values and Feature Probabilities to Identify Peptides from Tandem Mass Spectra
Ignat V. Shilov, Sean L. Seymour, Alpesh A. Patel, Alex Loboda, Wilfred H. Tang, Sean P. Keating, Christie L. Hunter, Lydia M. Nuwaysir, and Daniel A. Schaeffer - Immobilized Zirconium Ion Affinity Chromatography for Specific Enrichment of Phosphopeptides in Phosphoproteome Analysis
Shun Feng, Mingliang Ye, Houjiang Zhou, Xiaogang Jiang, Xingning Jiang, Hanfa Zou, and Bolin Gong - Human Proteome Organization Proteomics Standards Initiative: Data Standardization, a View on Developments and Policy
Lennart Martens, Sandra Orchard, Rolf Apweiler, and Henning Hermjakob
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Bioinformatics: Volume 23, Number 15, August 2007 - Mon, Aug 20, 11:23 PM
Submitted By: Patrick Kincaid
A new issue of Bioinformatics is now available. Here is a summary of the original papers. Links are provided to the on-line HTML and PDF files for the research articles. You may have to have a subscription to read the on-line articles.
- Isolated ZP-N domains constitute the N-terminal extensions of Zona Pellucida proteins
[Abstract], [Full Text], [Print PDF]
Isabelle Callebaut, Jean-Paul Mornon, and Philippe Monget - Predicting functionally important residues from sequence conservation
[Abstract], [FREE Full Text], [Print PDF]
John A. Capra and Mona Singh - RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment
[Abstract], [Full Text], [Print PDF]
Xing Xu, Yongmei Ji, and Gary D. Stormo - PALMA: mRNA to genome alignments using large margin algorithms
[Abstract], [FREE Full Text], [Print PDF]
Uta Schulze, Bettina Hepp, Cheng Soon Ong, and Gunnar Rätsch - An evaluation of automated homology modelling methods at low target–template sequence similarity
[Abstract], [Full Text], [Print PDF]
James A. R. Dalton and Richard M. Jackson - Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein–protein interactions
[Abstract], [Full Text], [Print PDF]
Mainak Guharoy and Pinak Chakrabarti - Exploring sequence-structure relationships in the tyrosine kinome space: functional classification of the binding specificity mechanisms for cancer therapeutics
[Abstract], [Full Text], [Print PDF]
Gennady M. Verkhivker - Mining co-regulated gene profiles for the detection of functional associations in gene expression data
[Abstract], [Full Text]