%A Jones P
%A Cote RG
%A Cho SY
%A Klie S
%A Martens L
%A Quinn AF
%A Thorneycroft D
%A Hermjakob H
%T PRIDE: new developments and new datasets
%0 Journal Article
%D 2008
%J Nucl Acids Res
%P D878-83
%V 36
%N Database issue
%U http://dx.doi.org/10.1093/nar/gkm1021

%A Sardiu ME
%A Cai Y
%A Jin J
%A Swanson SK
%A Conaway RC
%A Conaway JW
%A Florens L
%A Washburn MP
%T Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics
%0 Journal Article
%D 2008
%J Proc Natl Acad Sci U S A
%P 1454-9
%V 105
%N 5
%U http://dx.doi.org/10.1073/pnas.0706983105

%A Mulder NJ
%A Kersey P
%A Pruess M
%A Apweiler R
%T In Silico Characterization of Proteins: UniProt, InterPro and Integr8
%0 Journal Article
%D 2008
%J Mol Biotechnol
%P 165-77
%V 38
%N 2
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18219596&dopt=Abstract

%A Ido Ginodi
%A Tal Vider-Shalit
%A Lea Tsaban
%A Yoram Louzoun
%T Precise score for the prediction of peptides cleaved by the proteasome
%0 Journal Article
%D 2008
%J Bioinformatics
%P 477-483
%V 24
%N 4
%U http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/4/477?etoc

%A Pham TV
%A van de Wiel MA
%A Jimenez CR
%T Support vector machine approach to separate control and breast cancer serum samples
%0 Journal Article
%D 
%J 
%P -
%V 
%N 
%U http://www.bepress.com/sagmb/vol7/iss2/art11

%A Mulder N
%A Apweiler R
%T InterPro and InterProScan: Tools for Protein Sequence Classification and Comparison
%0 Journal Article
%D 2007
%J Methods Mol Biol
%P 59-70
%V 396
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18025686&dopt=Abstract

%A Bocker S
%A Makinen V
%T Combinatorial approaches for mass spectra recalibration
%0 Journal Article
%D 2008
%J IEEE/ACM Trans Comput Biol Bioinform
%P 91-100
%V 5
%N 1
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18245878&dopt=Abstract

%A Mahal LK
%T Glycomics: towards bioinformatic approaches to understanding glycosylation
%0 Journal Article
%D 2008
%J Anticancer Agents Med Chem
%P 37-51
%V 8
%N 1
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18220504&dopt=Abstract

%A Meuleman W
%A Engwegen JY
%A Gast MC
%A Beijnen JH
%A Reinders MJ
%A Wessels LF
%T Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data
%0 Journal Article
%D 
%J 
%P -
%V 
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18257918&dopt=Abstract

%A Mathias Vandenbogaert
%A Sébastien Li-Thiao-Té
%A Hans-Michael Kaltenbach
%A Runxuan Zhang
%A Tero Aittokallio
%A Benno Schwikowski
%T Alignment of LC-MS images, with applications to biomarker discovery and protein identification
%0 Journal Article
%D 2008
%J PROTEOMICS
%P 650-672
%V 8
%N 4
%U http://dx.doi.org/10.1002/pmic.200700791

%A Ye J
%A Liu H
%A Kirmiz C
%A Lebrilla CB
%A Rocke DM
%T On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve
%0 Journal Article
%D 
%J 
%P -
%V 
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18076765&dopt=Abstract

%A Smit S
%A Hoefsloot HC
%A Smilde AK
%T Statistical data processing in clinical proteomics
%0 Journal Article
%D 2007
%J J Chromatogr B Analyt Technol Biomed Life Sci
%P -
%V 
%N 
%U http://dx.doi.org/10.1016/j.jchromb.2007.10.042
%8 Nov 4, 2007

%A Mavroudi
%A Seferina; Papadimitriou
%A Stergios; Kossida
%A Sophia; Likothanassis
%A Spyridon D.; Vlahou
%A Antonia
%T Computational Methods and Algorithms for Mass-Spectrometry Based Differential Proteomics
%0 Journal Article
%D 2007
%J Current Proteomics
%P 223-234
%V 4
%N 4
%U http://www.ingentaconnect.com/content/ben/cp/2007/00000004/00000004/art00004

%A Gerassimos Bastas
%A Seshi R. Sompuram
%A Brian Pierce
%A Kodela Vani
%A Steven A. Bogen
%T Bioinformatic Requirements for Protein Database Searching Using Predicted Epitopes from Disease-associated Antibodies
%0 Journal Article
%D 2008
%J Mol Cell Proteomics
%P 247-256
%V 7
%N 2
%U http://www.mcponline.org/cgi/content/abstract/7/2/247?etoc

%A Jeffrey S. Morris
%A Brittan N. Clark
%A Howard B. Gutstein
%T Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data
%0 Journal Article
%D 2008
%J Bioinformatics
%P 529-536
%V 24
%N 4
%U http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/4/529?etoc

%A Hoefsloot HC
%A Smit S
%A Smilde AK
%T A classification model for the leiden proteomics competition
%0 Journal Article
%D 
%J 
%P -
%V 
%N 
%U http://www.bepress.com/sagmb/vol7/iss2/art8

%A Gong W
%A Zhou D
%A Ren Y
%A Wang Y
%A Zuo Z
%A Shen Y
%A Xiao F
%A Zhu Q
%A Hong A
%A Zhou X
%A Gao X
%A Li T
%T PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains
%0 Journal Article
%D 2008
%J Nucl Acids Res
%P D679-83
%V 36
%N Database issue
%U http://dx.doi.org/10.1093/nar/gkm854

%A Heidema AG
%A Nagelkerke N
%T Developing a discrimination rule between breast cancer patients and controls using proteomics mass spectrometric data: a three-step approach
%0 Journal Article
%D 
%J 
%P -
%V 
%N 
%U http://www.bepress.com/sagmb/vol7/iss2/art4

%A Melissa R. Thompson
%A Dorothea K. Thompson
%A Robert L. Hettich
%T Systematic Assessment of the Benefits and Caveats in Mining Microbial Post-Translational Modifications from Shotgun Proteomic Data: The Response of Shewanella oneidensis to Chromate Exposure
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 648-658
%V 7
%N 02
%U http://dx.doi.org/10.1021/pr070531n

%A Droit A
%A Hunter JM
%A Rouleau M
%A Ethier C
%A Picard-Cloutier A
%A Bourgais D
%A Poirier GG
%T PARPs Database: A LIMS systems for protein-protein interaction data mining or Laboratory Information management system
%0 Journal Article
%D 
%J 
%P -
%V 
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18093328&dopt=Abstract

%A Quentin Kaas
%A Jan-C. Westermann
%A Reena Halai
%A Conan K. L. Wang
%A David J. Craik
%T ConoServer, a database for conopeptide sequences and structures
%0 Journal Article
%D 2008
%J Bioinformatics
%P 445-446
%V 24
%N 3
%U http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/3/445?etoc

%A Goeman JJ
%T Autocorrelated logistic ridge regression for prediction based on proteomics spectra
%0 Journal Article
%D 
%J 
%P -
%V 
%N 
%U http://www.bepress.com/sagmb/vol7/iss2/art10

%A Skrabanek L
%A Saini HK
%A Bader GD
%A Enright AJ
%T Computational prediction of protein-protein interactions
%0 Journal Article
%D 2008
%J Mol Biotechnol
%P 1-17
%V 38
%N 1
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18095187&dopt=Abstract

%A Marengo E
%A Robotti E
%A Bobba M
%A Milli A
%A Campostrini N
%A Righetti SC
%A Cecconi D
%A Righetti PG
%T Application of partial least squares discriminant analysis and variable selection procedures: a 2D-PAGE proteomic study
%0 Journal Article
%D 2008
%J Anal Bioanal Chem
%P -
%V 
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18224487&dopt=Abstract
%8 Jan 29, 2008

%A Sprenger J
%A Lynn Fink J
%A Karunaratne S
%A Hanson K
%A Hamilton NA
%A Teasdale RD
%T LOCATE: a mammalian protein subcellular localization database
%0 Journal Article
%D 2008
%J Nucl Acids Res
%P D230-3
%V 36
%N Database issue
%U http://dx.doi.org/10.1093/nar/gkm950

%A Barrett JH
%A Cairns DA
%T Application of the random forest classification method to peaks detected from mass spectrometric proteomic profiles of cancer patients and controls
%0 Journal Article
%D 
%J 
%P -
%V 
%N 
%U http://www.bepress.com/sagmb/vol7/iss2/art4

%A Seungjin Na
%A Eunok Paek
%A Cheolju Lee
%T CIFTER: Automated Charge-State Determination for Peptide Tandem Mass Spectra
%0 Journal Article
%D 2008
%J ANALYTICAL CHEMISTRY
%P 1520-1528
%V 80
%N 5
%U http://dx.doi.org/10.1021/ac702038q

%A Sebastian Bocker
%A Zsuzsanna Liptak
%A Marcel Martin
%A Anton Pervukhin
%A Henner Sudek
%T DECOMP--from interpreting Mass Spectrometry peaks to solving the Money Changing Problem
%0 Journal Article
%D 2008
%J Bioinformatics
%P 591-593
%V 24
%N 4
%U http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/4/591?etoc

%A Mertens B
%T Organizing a competition on clinical mass spectrometry based proteomic diagnosis
%0 Journal Article
%D 
%J 
%P -
%V 
%N 
%U http://www.bepress.com/sagmb/vol7/iss2/art3

%A Datta S
%T Classification of breast cancer versus normal samples from mass spectrometry profiles using linear discriminant analysis of important features selected by random forest
%0 Journal Article
%D 
%J 
%P -
%V 
%N 
%U http://www.bepress.com/sagmb/vol7/iss2/art7

%A Mistry J
%A Finn R
%T Pfam: a domain-centric method for analyzing proteins and proteomes
%0 Journal Article
%D 2007
%J Methods Mol Biol
%P 43-58
%V 396
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18025685&dopt=Abstract

%A Higdon R
%A Hogan JM
%A Kolker N
%A van Belle G
%A Kolker E
%T Experiment-specific estimation of Peptide identification probabilities using a randomized database
%0 Journal Article
%D 2007
%J OMICS
%P 351-66
%V 11
%N 4
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18092908&dopt=Abstract

%A Thitiwan Srinark
%A Chandra Kambhamettu
%T An image analysis suite for spot detection and spot matching in two-dimensional electrophoresis gels
%0 Journal Article
%D 2008
%J ELECTROPHORESIS
%P 706-715
%V 29
%N 3
%U http://dx.doi.org/10.1002/elps.200700244

%A Zhang
%A Xiang; Oh
%A Cheolhwan; Riley
%A Catherine P.; Buck
%A Charles
%T Current Status of Computational Approaches for Protein Identification Using Tandem Mass Spectra
%0 Journal Article
%D 2007
%J Current Proteomics
%P 121-130
%V 4
%N 3
%U http://www.ingentaconnect.com/content/ben/cp/2007/00000004/00000003/art00001

%A Bryan G. Fry
%A Holger Scheib
%A Louise van der Weerd
%A Bruce Young
%A JudithMcNaughtan
%A S. F. Ryan Ramjan
%A Nicolas Vidal
%A Robert E. Poelmann
%A Janette A. Norman
%T Evolution of an Arsenal: Structural and Functional Diversification of the Venom System in the Advanced Snakes (Caenophidia)
%0 Journal Article
%D 2008
%J Mol Cell Proteomics
%P 215-246
%V 7
%N 2
%U http://www.mcponline.org/cgi/content/abstract/7/2/215?etoc