TY  - JOUR
A1  - Sandra Orchard
A1  - Christine Hoogland
A1  - Amos Bairoch
A1  - Martin Eisenacher
A1  - Hans-Joachim Kraus
A1  - Pierre-Alain Binz
T1  - Managing the Data Explosion A Report on the HUPO-PSI Workshop August 2008, Amsterdam, The Netherlands
JO  - PROTEOMICS
Y1  - 2009
SP  - 499
EP  - 501
VL  - 9
IS  - 3
UR  - http://dx.doi.org/10.1002/pmic.200800838
ER  - 

TY  - JOUR
A1  - Madrid-Aliste CJ
A1  - Dybas JM
A1  - Hogue Angeletti R
A1  - Weiss LM
A1  - Kim K
A1  - Simon I
A1  - Fiser A
T1  - EPIC-DB: a proteomics database for studying Apicomplexan organisms
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19159464&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Sarah Dunn Keene
A1  - Todd M. Greco
A1  - Ioannis Parastatidis
A1  - Seon-Hwa Lee
A1  - Ethan G. Hughes
A1  - Rita J. Balice-Gordon
A1  - David W. Speicher
A1  - Harry Ischiropoulos
T1  - Mass spectrometric and computational analysis of cytokine-induced alterations in the astrocyte secretome
JO  - PROTEOMICS
Y1  - 2009
SP  - 768
EP  - 782
VL  - 9
IS  - 3
UR  - http://dx.doi.org/10.1002/pmic.200800385
ER  - 

TY  - JOUR
A1  - Yang Y
A1  - Adelstein SJ
A1  - Kassis AI
T1  - Target discovery from data mining approaches
JO  - Drug Discov Today
Y1  - 2009
SP  - 147
EP  - 54
VL  - 14
IS  - 3-4
UR  - http://dx.doi.org/10.1016/j.drudis.2008.12.005
ER  - 

TY  - JOUR
A1  - Warren Albertin
A1  - Olivier Langella
A1  - Johann Joets
A1  - Luc Négroni
A1  - Michel Zivy
A1  - Catherine Damerval
A1  - Hervé Thiellement
T1  - Comparative proteomics of leaf, stem, and root tissues of synthetic Brassica napus
JO  - PROTEOMICS
Y1  - 2009
SP  - 793
EP  - 799
VL  - 9
IS  - 3
UR  - http://dx.doi.org/10.1002/pmic.200800479
ER  - 

TY  - JOUR
A1  - Browne F
A1  - Wang H
A1  - Zheng H
A1  - Azuaje F
T1  - GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19171033&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Jussi Salmi
A1  - Tuula A. Nyman
A1  - Olli S. Nevalainen
A1  - Tero Aittokallio
T1  - Filtering strategies for improving protein identification in high-throughput MS/MS studies
JO  - PROTEOMICS
Y1  - 2009
SP  - 848
EP  - 860
VL  - 9
IS  - 4
UR  - http://dx.doi.org/10.1002/pmic.200800517
ER  - 

TY  - JOUR
A1  - Christopher Reynolds
A1  - David Damerell
A1  - Susan Jones
T1  - ProtorP: a protein-protein interaction analysis server
JO  - Bioinformatics
Y1  - 2009
SP  - 413
EP  - 414
VL  - 25
IS  - 3
UR  - http://dx.doi.org/10.1093/bioinformatics/btn584
ER  - 

TY  - JOUR
A1  - Yanofsky CM
A1  - Kearney RE
A1  - Lesimple S
A1  - Bergeron JJ
A1  - Boismenu D
A1  - Carrillo B
A1  - Bell AW
T1  - A Bayesian approach to peptide identification using Accurate Mass and Time tags from LC-FTICR-MS proteomics experiments
JO  - Conf Proc IEEE Eng Med Biol Soc
Y1  - 2008
SP  - 3775
EP  - 3778
VL  - 1
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19163533&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Simon Rogers
A1  - Richard A. Scheltema
A1  - Mark Girolami
A1  - Rainer Breitling
T1  - Probabilistic assignment of formulas to mass peaks in metabolomics experiments
JO  - Bioinformatics
Y1  - 2009
SP  - 512
EP  - 518
VL  - 25
IS  - 4
UR  - http://dx.doi.org/10.1093/bioinformatics/btn642
ER  - 

TY  - JOUR
A1  - Jennifer A. Mead
A1  - Luca Bianco
A1  - Conrad Bessant
T1  - Recent developments in public proteomic MS repositories and pipelines
JO  - PROTEOMICS
Y1  - 2009
SP  - 861
EP  - 881
VL  - 9
IS  - 4
UR  - http://dx.doi.org/10.1002/pmic.200800553
ER  - 

TY  - JOUR
A1  - Valente AX
A1  - Roberts SB
A1  - Buck GA
A1  - Gao Y
T1  - Functional organization of the yeast proteome by a yeast interactome map
JO  - Proc Natl Acad Sci U S A
Y1  - 2009/01/21
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19164585&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Nils Gehlenborg
A1  - Wei Yan
A1  - Inyoul Y. Lee
A1  - Hyuntae Yoo
A1  - Kay Nieselt
A1  - Daehee Hwang
A1  - Ruedi Aebersold
A1  - Leroy Hood
T1  - Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data
JO  - Bioinformatics
Y1  - 2009
SP  - 682
EP  - 683
VL  - 25
IS  - 5
UR  - http://dx.doi.org/10.1093/bioinformatics/btp005
ER  - 

TY  - JOUR
A1  - Tarasova IA
A1  - Guryča V
A1  - Pridatchenko ML
A1  - Gorshkov AV
A1  - Kieffer-Jaquinod S
A1  - Evreinov VV
A1  - Masselon CD
A1  - Gorshkov MV
T1  - Standardization of retention time data for AMT tag proteomics database generation
JO  - J Chromatogr B Analyt Technol Biomed Life Sci
Y1  - 2008/12/25
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19144581&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Andrew R. Jones
A1  - Jennifer A. Siepen
A1  - Simon J. Hubbard
A1  - Norman W. Paton
T1  - Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines
JO  - PROTEOMICS
Y1  - 2009
SP  - 1220
EP  - 1229
VL  - 9
IS  - 5
UR  - http://dx.doi.org/10.1002/pmic.200800473
ER  - 

TY  - JOUR
A1  - Schmidt F
A1  - Schmid M
A1  - Thiede B
A1  - Pleiszner KP
A1  - Bohme M
A1  - Jungblut PR
T1  - Assembling proteomics data as a prerequisite for the analysis of large scale experiments
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19166578&dopt=Abstract
ER  - 

TY  - JOUR
A1  - David Goldberg
A1  - Marshall Bern
A1  - Simon J. North
A1  - Stuart M. Haslam
A1  - Anne Dell
T1  - Glycan family analysis for deducing N-glycan topology from single MS
JO  - Bioinformatics
Y1  - 2009
SP  - 365
EP  - 371
VL  - 25
IS  - 3
UR  - http://dx.doi.org/10.1093/bioinformatics/btn636
ER  - 

TY  - JOUR
A1  - Martina Stessl
A1  - Christian R. Noe
A1  - Bodo Lachmann
T1  - Influence of image-analysis software on quantitation of two-dimensional gel electrophoresis data
JO  - ELECTROPHORESIS
Y1  - 2009
SP  - 325
EP  - 328
VL  - 30
IS  - 2
UR  - http://dx.doi.org/10.1002/elps.200800213
ER  - 

TY  - JOUR
A1  - Kiel JA
A1  - van den Berg MA
A1  - Fusetti F
A1  - Poolman B
A1  - Bovenberg RA
A1  - Veenhuis M
A1  - van der Klei IJ
T1  - Matching the proteome to the genome: the microbody of penicillin-producing Penicillium chrysogenum cells
JO  - Funct Integr Genomics
Y1  - 2009/01/21
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://dx.doi.org/10.1007/s10142-009-0110-6
ER  - 

TY  - JOUR
A1  - Magnus Ř. Arntzen
A1  - Christoffer Leif Osland
A1  - Christopher Rasch-Olsen Raa
A1  - Reidun Kopperud
A1  - Stein-Ove Dřskeland
A1  - Aurélia E. Lewis
A1  - Clive S. D'Santos
T1  - POSTMan (POST-translational modification analysis), a software application for PTM discovery
JO  - PROTEOMICS
Y1  - 2009
SP  - 1400
EP  - 1406
VL  - 9
IS  - 5
UR  - http://dx.doi.org/10.1002/pmic.200800500
ER  - 

TY  - JOUR
A1  - Wright JC
A1  - Hubbard SJ
T1  - Recent developments in proteome informatics for mass spectrometry analysis
JO  - Comb Chem High Throughput Screen
Y1  - 2009
SP  - 194
EP  - 202
VL  - 12
IS  - 2
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19199887&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Davide Bolchini
A1  - Anthony Finkelstein
A1  - Vito Perrone
A1  - Sylvia Nagl
T1  - Better bioinformatics through usability analysis
JO  - Bioinformatics
Y1  - 2009
SP  - 406
EP  - 412
VL  - 25
IS  - 3
UR  - http://dx.doi.org/10.1093/bioinformatics/btn633
ER  - 

TY  - JOUR
A1  - Webb-Robertson BJ
A1  - McCue LA
A1  - Beagley N
A1  - McDermott JE
A1  - Wunschel DS
A1  - Varnum SM
A1  - Hu JZ
A1  - Isern NG
A1  - Buchko GW
A1  - Mcateer K
A1  - Pounds JG
A1  - Skerrett SJ
A1  - Liggitt D
A1  - Frevert CW
T1  - A Bayesian integration model of high-throughput proteomics and metabolomics data for improved early detection of microbial infections
JO  - Pac Symp Biocomput
Y1  - 2009
SP  - 451
EP  - 63
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19209722&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Daniel Schwartz
A1  - Michael F. Chou
A1  - George M. Church
T1  - Predicting Protein Post-translational Modifications Using Meta-analysis of Proteome Scale Data Sets
JO  - Mol Cell Proteomics
Y1  - 2009
SP  - 365
EP  - 379
VL  - 8
IS  - 2
UR  - http://www.mcponline.org/cgi/content/abstract/8/2/365?etoc
ER  - 

TY  - JOUR
A1  - Kluge B
A1  - Gambin A
A1  - Niemiro W
T1  - Modeling exopeptidase activity from LC-MS data
JO  - J Comput Biol
Y1  - 2009
SP  - 395
EP  - 406
VL  - 16
IS  - 2
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19193154&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Yun D
A1  - Lu H
A1  - Yang P
A1  - He F
T1  - Spectral quality assessment and application for gel-based matrix-assisted laser desorption ionization-time of flight tandem mass spectrometer
JO  - Anal Chim Acta
Y1  - 2009
SP  - 158
EP  - 65
VL  - 634
IS  - 2
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19185114&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Wright JC
A1  - Sugden D
A1  - Francis-McIntyre S
A1  - Riba-Garcia I
A1  - Gaskell SJ
A1  - Grigoriev IV
A1  - Baker SE
A1  - Beynon RJ
A1  - Hubbard SJ
T1  - Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19193216&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Theodore Alexandrov
A1  - Jens Decker
A1  - Bart Mertens
A1  - Andre M. Deelder
A1  - Rob A. E. M. Tollenaar
A1  - Peter Maass
A1  - Herbert Thiele
T1  - Biomarker discovery in MALDI-TOF serum protein profiles using discrete wavelet transformation
JO  - Bioinformatics
Y1  - 2009
SP  - 643
EP  - 649
VL  - 25
IS  - 5
UR  - http://dx.doi.org/10.1093/bioinformatics/btn662
ER  - 

TY  - JOUR
A1  - Dudley JT
A1  - Butte AJ
T1  - Identification of discriminating biomarkers for human disease using integrative network biology
JO  - Pac Symp Biocomput
Y1  - 2009
SP  - 27
EP  - 38
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19209693&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Yusuke Miyao
A1  - Kenji Sagae
A1  - Rune Saetre
A1  - Takuya Matsuzaki
A1  - Jun'ichi Tsujii
T1  - Evaluating contributions of natural language parsers to protein-protein interaction extraction
JO  - Bioinformatics
Y1  - 2009
SP  - 394
EP  - 400
VL  - 25
IS  - 3
UR  - http://dx.doi.org/10.1093/bioinformatics/btn631
ER  - 

TY  - JOUR
A1  - Tomasz B?czek
A1  - Roman Kaliszan
T1  - Predictions of peptides' retention times in reversed-phase liquid chromatography as a new supportive tool to improve protein identification in proteomics
JO  - PROTEOMICS
Y1  - 2009
SP  - 835
EP  - 847
VL  - 9
IS  - 4
UR  - http://dx.doi.org/10.1002/pmic.200800544
ER  -