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%T Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC-MS/MS data
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%J PROTEOMICS
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%U http://dx.doi.org/10.1002/pmic.200500921

%A Julie L. Morrison
%A Rainer Breitling
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%A David R.  Gilbert
%T A lock-and-key model for protein-protein interactions
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%U http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/16/2012?etoc

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%T Identification of biomarkers from mass spectrometry data using a "common" peak approach
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%A Andreas M. Boehm
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%T A comprehensive dictionary of protein accession codes for complete protein accession identifier alias resolving
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%A Yao H
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%T Rank information: A structure-independent measure of evolutionary trace quality that improves identification of protein functional sites
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%T Identification of biomarkers from mass spectrometry data using a "common" peak approach
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%A Hiller K
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%T JVirGel 2.0: computational prediction of proteomes separated via two dimensional gel electrophoresis under consideration of membrane and secreted proteins
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%U http://dx.doi.org/10.1093/bioinformatics/btl409

%A Kuo-Chen Chou and Hong-Bin Shen
%T Predicting Eukaryotic Protein Subcellular Location by Fusing Optimized Evidence-Theoretic K-Nearest Neighbor Classifiers
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%J JOURNAL OF PROTEOME RESEARCH
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%T Viewing the proteome from oligopeptides and prediction of protein function
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%T Huge proteins in the human proteome and their participation in hereditary diseases
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%A Natalie Wielsch
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%T Rapid Validation of Protein Identifications with the Borderline Statistical Confidence via De Novo Sequencing and MS BLAST Searches
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%A Pan Du
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%T Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching
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%T The ciliary proteome database: an integrated community resource for the genetic and functional dissection of cilia
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%A Jeremy Widmann
%A Micah Hamady
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%T DivergentSet, a Tool for Picking Non-redundant Sequences from Large Sequence Collections
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%T IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics
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%U http://dx.doi.org/10.1093/bioinformatics/btl410

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%T The Pathway Tools cellular overview diagram and Omics Viewer
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%T A statistical method for chromatographic alignment of LC-MS data
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%U http://dx.doi.org/10.1093/biostatistics/kxl015

%A John T. Prince and Edward M. Marcotte
%T Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpolated Warping
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%U http://dx.doi.org/10.1021/ac0605344

%A Barbara E. Frewen
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%A William Stafford Noble
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%T Analysis of Peptide MS/MS Spectra from Large-Scale Proteomics Experiments Using Spectrum Libraries
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%A Zhi Liang
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%T NetAlign: a web-based tool for comparison of protein interaction networks
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%A James Vlasblom
%A Samuel Wu
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%A Chris Orsi
%A Shoshana J. Wodak
%T GenePro: a cytoscape plug-in for advanced visualization and analysis of interaction networks
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%U http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/17/2178?etoc

%T TOOLbox: PROMPT for comparisons | msInspect | Rapid peptide identifications | MeMo for metabolomics data
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%U http://pubs.acs.org/subscribe/journals/jprobs/5/i09/html/0906toolbox.html

%A György Babnigg
%A Carol S. Giometti
%T A database of unique protein sequence identifiers for proteome studies
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%U http://dx.doi.org/10.1002/pmic.200600032

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%T Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures
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%U http://dx.doi.org/10.1002/prot.21163

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%T Concept of Sample in OMICS Technology
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%A Taylor CF
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%T The Work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI)
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%A Mei Huang
%A Tong Chen
%A ZhuLong Chan
%T An evaluation for cross-species proteomics research by publicly available expressed sequence tag database search using tandem mass spectral data
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%U http://dx.doi.org/10.1002/rcm.2631

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%T Databases and resources for in silico proteome analysis
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%T General framework for developing and evaluating database scoring algorithms using the TANDEM search engine
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%U http://dx.doi.org/10.1093/bioinformatics/btl379

%A Kui Lin
%A Lei Zhu
%A Da-Yong Zhang
%T An initial strategy for comparing proteins at the domain architecture level
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%U http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/17/2081?etoc

%A Kazuyasu Fujii
%A Tadashi Kondo
%A Masayo Yamada
%A Keiji Iwatsuki
%A Setsuo Hirohashi
%T Toward a comprehensive quantitative proteome database: protein expression map of lymphoid neoplasms by 2-D DIGE and MS
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%D 2006
%J PROTEOMICS
%P 4856-4876
%V 6
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%U http://dx.doi.org/10.1002/pmic.200600097