TY  - JOUR
A1  - Jones P
A1  - Cote RG
A1  - Cho SY
A1  - Klie S
A1  - Martens L
A1  - Quinn AF
A1  - Thorneycroft D
A1  - Hermjakob H
T1  - PRIDE: new developments and new datasets
JO  - Nucl Acids Res
Y1  - 2008
SP  - D878
EP  - 83
VL  - 36
IS  - Database issue
UR  - http://dx.doi.org/10.1093/nar/gkm1021
ER  - 

TY  - JOUR
A1  - Sardiu ME
A1  - Cai Y
A1  - Jin J
A1  - Swanson SK
A1  - Conaway RC
A1  - Conaway JW
A1  - Florens L
A1  - Washburn MP
T1  - Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics
JO  - Proc Natl Acad Sci U S A
Y1  - 2008
SP  - 1454
EP  - 9
VL  - 105
IS  - 5
UR  - http://dx.doi.org/10.1073/pnas.0706983105
ER  - 

TY  - JOUR
A1  - Mulder NJ
A1  - Kersey P
A1  - Pruess M
A1  - Apweiler R
T1  - In Silico Characterization of Proteins: UniProt, InterPro and Integr8
JO  - Mol Biotechnol
Y1  - 2008
SP  - 165
EP  - 77
VL  - 38
IS  - 2
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18219596&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Ido Ginodi
A1  - Tal Vider-Shalit
A1  - Lea Tsaban
A1  - Yoram Louzoun
T1  - Precise score for the prediction of peptides cleaved by the proteasome
JO  - Bioinformatics
Y1  - 2008
SP  - 477
EP  - 483
VL  - 24
IS  - 4
UR  - http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/4/477?etoc
ER  - 

TY  - JOUR
A1  - Pham TV
A1  - van de Wiel MA
A1  - Jimenez CR
T1  - Support vector machine approach to separate control and breast cancer serum samples
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.bepress.com/sagmb/vol7/iss2/art11
ER  - 

TY  - JOUR
A1  - Mulder N
A1  - Apweiler R
T1  - InterPro and InterProScan: Tools for Protein Sequence Classification and Comparison
JO  - Methods Mol Biol
Y1  - 2007
SP  - 59
EP  - 70
VL  - 396
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18025686&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Bocker S
A1  - Makinen V
T1  - Combinatorial approaches for mass spectra recalibration
JO  - IEEE/ACM Trans Comput Biol Bioinform
Y1  - 2008
SP  - 91
EP  - 100
VL  - 5
IS  - 1
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18245878&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Mahal LK
T1  - Glycomics: towards bioinformatic approaches to understanding glycosylation
JO  - Anticancer Agents Med Chem
Y1  - 2008
SP  - 37
EP  - 51
VL  - 8
IS  - 1
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18220504&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Meuleman W
A1  - Engwegen JY
A1  - Gast MC
A1  - Beijnen JH
A1  - Reinders MJ
A1  - Wessels LF
T1  - Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18257918&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Mathias Vandenbogaert
A1  - Sébastien Li-Thiao-Té
A1  - Hans-Michael Kaltenbach
A1  - Runxuan Zhang
A1  - Tero Aittokallio
A1  - Benno Schwikowski
T1  - Alignment of LC-MS images, with applications to biomarker discovery and protein identification
JO  - PROTEOMICS
Y1  - 2008
SP  - 650
EP  - 672
VL  - 8
IS  - 4
UR  - http://dx.doi.org/10.1002/pmic.200700791
ER  - 

TY  - JOUR
A1  - Ye J
A1  - Liu H
A1  - Kirmiz C
A1  - Lebrilla CB
A1  - Rocke DM
T1  - On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18076765&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Smit S
A1  - Hoefsloot HC
A1  - Smilde AK
T1  - Statistical data processing in clinical proteomics
JO  - J Chromatogr B Analyt Technol Biomed Life Sci
Y1  - 2007/11/4
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://dx.doi.org/10.1016/j.jchromb.2007.10.042
ER  - 

TY  - JOUR
A1  - Mavroudi
A1  - Seferina; Papadimitriou
A1  - Stergios; Kossida
A1  - Sophia; Likothanassis
A1  - Spyridon D.; Vlahou
A1  - Antonia
T1  - Computational Methods and Algorithms for Mass-Spectrometry Based Differential Proteomics
JO  - Current Proteomics
Y1  - 2007
SP  - 223
EP  - 234
VL  - 4
IS  - 4
UR  - http://www.ingentaconnect.com/content/ben/cp/2007/00000004/00000004/art00004
ER  - 

TY  - JOUR
A1  - Gerassimos Bastas
A1  - Seshi R. Sompuram
A1  - Brian Pierce
A1  - Kodela Vani
A1  - Steven A. Bogen
T1  - Bioinformatic Requirements for Protein Database Searching Using Predicted Epitopes from Disease-associated Antibodies
JO  - Mol Cell Proteomics
Y1  - 2008
SP  - 247
EP  - 256
VL  - 7
IS  - 2
UR  - http://www.mcponline.org/cgi/content/abstract/7/2/247?etoc
ER  - 

TY  - JOUR
A1  - Jeffrey S. Morris
A1  - Brittan N. Clark
A1  - Howard B. Gutstein
T1  - Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data
JO  - Bioinformatics
Y1  - 2008
SP  - 529
EP  - 536
VL  - 24
IS  - 4
UR  - http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/4/529?etoc
ER  - 

TY  - JOUR
A1  - Hoefsloot HC
A1  - Smit S
A1  - Smilde AK
T1  - A classification model for the leiden proteomics competition
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.bepress.com/sagmb/vol7/iss2/art8
ER  - 

TY  - JOUR
A1  - Gong W
A1  - Zhou D
A1  - Ren Y
A1  - Wang Y
A1  - Zuo Z
A1  - Shen Y
A1  - Xiao F
A1  - Zhu Q
A1  - Hong A
A1  - Zhou X
A1  - Gao X
A1  - Li T
T1  - PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains
JO  - Nucl Acids Res
Y1  - 2008
SP  - D679
EP  - 83
VL  - 36
IS  - Database issue
UR  - http://dx.doi.org/10.1093/nar/gkm854
ER  - 

TY  - JOUR
A1  - Heidema AG
A1  - Nagelkerke N
T1  - Developing a discrimination rule between breast cancer patients and controls using proteomics mass spectrometric data: a three-step approach
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.bepress.com/sagmb/vol7/iss2/art4
ER  - 

TY  - JOUR
A1  - Melissa R. Thompson
A1  - Dorothea K. Thompson
A1  - Robert L. Hettich
T1  - 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
JO  - JOURNAL OF PROTEOME RESEARCH
Y1  - 2008
SP  - 648
EP  - 658
VL  - 7
IS  - 02
UR  - http://dx.doi.org/10.1021/pr070531n
ER  - 

TY  - JOUR
A1  - Droit A
A1  - Hunter JM
A1  - Rouleau M
A1  - Ethier C
A1  - Picard-Cloutier A
A1  - Bourgais D
A1  - Poirier GG
T1  - PARPs Database: A LIMS systems for protein-protein interaction data mining or Laboratory Information management system
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18093328&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Quentin Kaas
A1  - Jan-C. Westermann
A1  - Reena Halai
A1  - Conan K. L. Wang
A1  - David J. Craik
T1  - ConoServer, a database for conopeptide sequences and structures
JO  - Bioinformatics
Y1  - 2008
SP  - 445
EP  - 446
VL  - 24
IS  - 3
UR  - http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/3/445?etoc
ER  - 

TY  - JOUR
A1  - Goeman JJ
T1  - Autocorrelated logistic ridge regression for prediction based on proteomics spectra
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.bepress.com/sagmb/vol7/iss2/art10
ER  - 

TY  - JOUR
A1  - Skrabanek L
A1  - Saini HK
A1  - Bader GD
A1  - Enright AJ
T1  - Computational prediction of protein-protein interactions
JO  - Mol Biotechnol
Y1  - 2008
SP  - 1
EP  - 17
VL  - 38
IS  - 1
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18095187&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Marengo E
A1  - Robotti E
A1  - Bobba M
A1  - Milli A
A1  - Campostrini N
A1  - Righetti SC
A1  - Cecconi D
A1  - Righetti PG
T1  - Application of partial least squares discriminant analysis and variable selection procedures: a 2D-PAGE proteomic study
JO  - Anal Bioanal Chem
Y1  - 2008/01/29
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18224487&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Sprenger J
A1  - Lynn Fink J
A1  - Karunaratne S
A1  - Hanson K
A1  - Hamilton NA
A1  - Teasdale RD
T1  - LOCATE: a mammalian protein subcellular localization database
JO  - Nucl Acids Res
Y1  - 2008
SP  - D230
EP  - 3
VL  - 36
IS  - Database issue
UR  - http://dx.doi.org/10.1093/nar/gkm950
ER  - 

TY  - JOUR
A1  - Barrett JH
A1  - Cairns DA
T1  - Application of the random forest classification method to peaks detected from mass spectrometric proteomic profiles of cancer patients and controls
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.bepress.com/sagmb/vol7/iss2/art4
ER  - 

TY  - JOUR
A1  - Seungjin Na
A1  - Eunok Paek
A1  - Cheolju Lee
T1  - CIFTER: Automated Charge-State Determination for Peptide Tandem Mass Spectra
JO  - ANALYTICAL CHEMISTRY
Y1  - 2008
SP  - 1520
EP  - 1528
VL  - 80
IS  - 5
UR  - http://dx.doi.org/10.1021/ac702038q
ER  - 

TY  - JOUR
A1  - Sebastian Bocker
A1  - Zsuzsanna Liptak
A1  - Marcel Martin
A1  - Anton Pervukhin
A1  - Henner Sudek
T1  - DECOMP--from interpreting Mass Spectrometry peaks to solving the Money Changing Problem
JO  - Bioinformatics
Y1  - 2008
SP  - 591
EP  - 593
VL  - 24
IS  - 4
UR  - http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/4/591?etoc
ER  - 

TY  - JOUR
A1  - Mertens B
T1  - Organizing a competition on clinical mass spectrometry based proteomic diagnosis
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.bepress.com/sagmb/vol7/iss2/art3
ER  - 

TY  - JOUR
A1  - Datta S
T1  - Classification of breast cancer versus normal samples from mass spectrometry profiles using linear discriminant analysis of important features selected by random forest
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.bepress.com/sagmb/vol7/iss2/art7
ER  - 

TY  - JOUR
A1  - Mistry J
A1  - Finn R
T1  - Pfam: a domain-centric method for analyzing proteins and proteomes
JO  - Methods Mol Biol
Y1  - 2007
SP  - 43
EP  - 58
VL  - 396
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18025685&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Higdon R
A1  - Hogan JM
A1  - Kolker N
A1  - van Belle G
A1  - Kolker E
T1  - Experiment-specific estimation of Peptide identification probabilities using a randomized database
JO  - OMICS
Y1  - 2007
SP  - 351
EP  - 66
VL  - 11
IS  - 4
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18092908&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Thitiwan Srinark
A1  - Chandra Kambhamettu
T1  - An image analysis suite for spot detection and spot matching in two-dimensional electrophoresis gels
JO  - ELECTROPHORESIS
Y1  - 2008
SP  - 706
EP  - 715
VL  - 29
IS  - 3
UR  - http://dx.doi.org/10.1002/elps.200700244
ER  - 

TY  - JOUR
A1  - Zhang
A1  - Xiang; Oh
A1  - Cheolhwan; Riley
A1  - Catherine P.; Buck
A1  - Charles
T1  - Current Status of Computational Approaches for Protein Identification Using Tandem Mass Spectra
JO  - Current Proteomics
Y1  - 2007
SP  - 121
EP  - 130
VL  - 4
IS  - 3
UR  - http://www.ingentaconnect.com/content/ben/cp/2007/00000004/00000003/art00001
ER  - 

TY  - JOUR
A1  - Bryan G. Fry
A1  - Holger Scheib
A1  - Louise van der Weerd
A1  - Bruce Young
A1  - JudithMcNaughtan
A1  - S. F. Ryan Ramjan
A1  - Nicolas Vidal
A1  - Robert E. Poelmann
A1  - Janette A. Norman
T1  - Evolution of an Arsenal: Structural and Functional Diversification of the Venom System in the Advanced Snakes (Caenophidia)
JO  - Mol Cell Proteomics
Y1  - 2008
SP  - 215
EP  - 246
VL  - 7
IS  - 2
UR  - http://www.mcponline.org/cgi/content/abstract/7/2/215?etoc
ER  -