%A Craig D. Wenger
%A Michael T. Boyne II
%A Jonathan T. Ferguson
%A Dana E. Robinson
%A Neil L. Kelleher
%T Versatile Online−Offline Engine for Automated Acquisition of High-Resolution Tandem Mass Spectra
%0 Journal Article
%D 2008
%J ANALYTICAL CHEMISTRY
%P 8055-8063
%V 80
%N 21
%U http://dx.doi.org/10.1021/ac8010704

%A Bringans S
%A Kendrick TS
%A Lui J
%A Lipscombe R
%T A comparative study of the accuracy of several de novo sequencing software packages for datasets derived by matrix-assisted laser desorption/ionisation and electrospray
%0 Journal Article
%D 2008
%J Rapid Commun Mass Spectrom
%P 3450-3454
%V 22
%N 21
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18837480&dopt=Abstract

%A Hammami R
%A Ben Hamida J
%A Vergoten G
%A Fliss I
%T PhytAMP: a database dedicated to antimicrobial plant peptides
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%D 2008
%J Nucleic Acids Res
%P -
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%8 Oct 4, 2008

%A Sun Q
%A Zybailov B
%A Majeran W
%A Friso G
%A Olinares PD
%A van Wijk KJ
%T PPDB, the Plant Proteomics Database at Cornell
%0 Journal Article
%D 2008
%J Nucleic Acids Res
%P -
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%N 
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%8 Oct 2, 2008

%A Wolfgang Hoehenwarter
%A Joost T. van Dongen
%A Stefanie Wienkoop
%A Matthias Steinfath
%A Jan Hummel
%A Alexander Erban
%A Ronan Sulpice
%A Babette Regierer
%A Joachim Kopka
%A Peter Geigenberger
%A Wolfram Weckwerth
%T A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment
%0 Journal Article
%D 2008
%J PROTEOMICS
%P 4214-4225
%V 8
%N 20
%U http://dx.doi.org/10.1002/pmic.200701047

%A Hendrickson EL
%A Lamont RJ
%A Hackett M
%T Tools for Interpreting Large-scale Protein Profiling in Microbiology
%0 Journal Article
%D 2008
%J J Dent Res
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%V 87
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%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18946006&dopt=Abstract

%A Chatr-aryamontri A
%A Kerrien S
%A Khadake J
%A Orchard S
%A Ceol A
%A Licata L
%A Castagnoli L
%A Costa S
%A Derow C
%A Huntley R
%A Aranda B
%A Leroy C
%A Thorneycroft D
%A Apweiler R
%A Cesareni G
%A Hermjakob H
%T MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data
%0 Journal Article
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%A Swaney DL
%A McAlister GC
%A Coon JJ
%T Decision tree-driven tandem mass spectrometry for shotgun proteomics
%0 Journal Article
%D 2008
%J Nat Methods
%P 959-64
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%N 11
%U http://dx.doi.org/10.1038/nmeth.1260

%A Tonikian R
%A Zhang Y
%A Sazinsky SL
%A Currell B
%A Yeh JH
%A Reva B
%A Held HA
%A Appleton BA
%A Evangelista M
%A Wu Y
%A Xin X
%A Chan AC
%A Seshagiri S
%A Lasky LA
%A Sander C
%A Boone C
%A Bader GD
%A Sidhu SS
%T A specificity map for the PDZ domain family
%0 Journal Article
%D 
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%A Ahrens CH
%A Brunner E
%A Hafen E
%A Aebersold R
%A Basler K
%T A proteome catalog of Drosophila melanogaster: an essential resource for targeted quantitative proteomics
%0 Journal Article
%D 2007
%J Fly (Austin)
%P 182-6
%V 1
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%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18820430&dopt=Abstract

%A Monsellier E
%A Ramazzotti M
%A Taddei N
%A Chiti F
%T Aggregation propensity of the human proteome
%0 Journal Article
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%A Poh-Kuan Chong
%A Huiyin Lee
%A Jacklyn Wai-Fun Kong
%A Marie Chiew-Shia Loh
%A Chee-Hong Wong
%A Yoon-Pin Lim
%T Phosphoproteomics, oncogenic signaling and cancer research
%0 Journal Article
%D 2008
%J PROTEOMICS
%P 4370-4382
%V 8
%N 21
%U http://dx.doi.org/10.1002/pmic.200800051

%A Gnad F
%A Oroshi M
%A Birney E
%A Mann M
%T MAPU 2.0: high-accuracy proteomes mapped to genomes
%0 Journal Article
%D 2008
%J Nucleic Acids Res
%P -
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%U http://dx.doi.org/10.1093/nar/gkn773
%8 Oct 23, 2008

%A Andrew R. Jones and Sandra Orchard
%T Minimum Reporting Guidelines for Proteomics Released by the Proteomics Standards Initiative
%0 Journal Article
%D 2008
%J Mol Cell Proteomics
%P 2067-2068
%V 7
%N 10
%U http://www.mcponline.org/cgi/content/full/7/10/2067?etoc

%A Haleh Safavi
%A Nicolle Correa
%A Wei Xiong
%A Anindya Roy
%A Tülay Adali
%A Valeriy R. Korostyshevskiy
%A Carol C. Whisnant
%A Françoise Seillier-Moiseiwitsch
%T Independent component analysis of 2-D electrophoresis gels
%0 Journal Article
%D 2008
%J ELECTROPHORESIS
%P 4017-4026
%V 29
%N 19
%U http://dx.doi.org/10.1002/elps.200800028

%A Jimmy K. Eng
%A Bernd Fischer
%A Jonas Grossmann
%A Michael J. MacCoss
%T A Fast SEQUEST Cross Correlation Algorithm
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 4598-4602
%V 7
%N 10
%U http://dx.doi.org/10.1021/pr800420s

%A Candong Wei
%A Junping Peng
%A Zhaohui Xiong
%A Jian Yang
%A Jing Wang
%A Qi Jin
%T Subproteomic tools to increase genome annotation complexity
%0 Journal Article
%D 2008
%J PROTEOMICS
%P 4209-4213
%V 8
%N 20
%U http://dx.doi.org/10.1002/pmic.200800226

%A Kandasamy K
%A Keerthikumar S
%A Goel R
%A Mathivanan S
%A Patankar N
%A Shafreen B
%A Renuse S
%A Pawar H
%A Ramachandra YL
%A Acharya PK
%A Ranganathan P
%A Chaerkady R
%A Prasad TS
%A Pandey A
%T Human Proteinpedia: a unified discovery resource for proteomics research
%0 Journal Article
%D 2008
%J Nucleic Acids Res
%P -
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%8 Oct 23, 2008

%A Ali R. Vaezzadeh
%A Céline Hernandez
%A Oscar Vadas
%A Jacques J. M. Deshusses
%A Pierre Lescuyer
%A Frédérique Lisacek
%A Denis F. Hochstrasser
%T pICarver: A Software Tool and Strategy for Peptides Isoelectric Focusing
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 4336-4345
%V 7
%N 10
%U http://dx.doi.org/10.1021/pr8002672

%A Erik Bjorling and Mathias Uhlen
%T Antibodypedia, a Portal for Sharing Antibody and Antigen Validation Data
%0 Journal Article
%D 2008
%J Mol Cell Proteomics
%P 2028-2037
%V 7
%N 10
%U http://www.mcponline.org/cgi/content/abstract/7/10/2028?etoc

%A Lisa Berglund
%A Erik Bjorling
%A Per Oksvold
%A Linn Fagerberg
%A Anna Asplund
%A Cristina Al-Khalili Szigyarto
%A Anja Persson
%A Jenny Ottosson
%A Henrik Wernerus
%A Peter Nilsson
%A Emma Lundberg
%A Asa Sivertsson
%A Sanjay Navani
%A Kenneth Wester
%A Caroline Kampf
%A Sophia Hobe
%T A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies
%0 Journal Article
%D 2008
%J Mol Cell Proteomics
%P 2019-2027
%V 7
%N 10
%U http://www.mcponline.org/cgi/content/abstract/7/10/2019?etoc

%A Xia Cao and Alexey I. Nesvizhskii
%T Improved Sequence Tag Generation Method for Peptide Identification in Tandem Mass Spectrometry
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 4422-4434
%V 7
%N 10
%U http://dx.doi.org/10.1021/pr800400q

%A The UniProt Consortium
%T The Universal Protein Resource (UniProt) 2009
%0 Journal Article
%D 2008
%J Nucleic Acids Res
%P -
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%U http://dx.doi.org/10.1093/nar/gkn664
%8 Oct 4, 2008

%A Jian Liu
%A Alexandre Erassov
%A Patrick Halina
%A Myra Canete
%A Nguyen Dinh Vo
%A Clement Chung
%A Gerard Cagney
%A Alexandr Ignatchenko
%A Vincent Fong
%A Andrew Emili
%T Sequential Interval Motif Search: Unrestricted Database Surveys of Global MS/MS Data Sets for Detection of Putative Post-Translational Modifications
%0 Journal Article
%D 2008
%J ANALYTICAL CHEMISTRY
%P 7846-7854
%V 80
%N 20
%U http://dx.doi.org/10.1021/ac8009017

%A XiaoChun Xu
%A Dong Yu
%A Wei Fang
%A Yushao Cheng
%A Ziliang Qian
%A WenCong Lu
%A Yudong Cai
%A Kaiyan Feng
%T Prediction of Peptidase Category Based on Functional Domain Composition
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 4521-4524
%V 7
%N 10
%U http://dx.doi.org/10.1021/pr800292w

%A Suresh Mathivanan and Akhilesh Pandey
%T Human Proteinpedia as a Resource for Clinical Proteomics
%0 Journal Article
%D 2008
%J Mol Cell Proteomics
%P 2038-2047
%V 7
%N 10
%U http://www.mcponline.org/cgi/content/abstract/7/10/2038?etoc

%A Rodríguez-Pérez MA
%A Medina-Aunon A
%A Encarnación-Guevara SM
%A Bernal-Silvia S
%A Barrera-Saldaña H
%A Albar-Ramírez JP
%T In silico analysis of protein neoplastic biomarkers for cervix and uterine cancer
%0 Journal Article
%D 2008
%J Clin Transl Oncol
%P 604-17
%V 10
%N 10
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18940741&dopt=Abstract

%A Xudong Yao
%A Pamela Diego
%A Alexis A. Ramos
%A Yu Shi
%T Averagine-Scaling Analysis and Fragment Ion Mass Defect Labeling in Peptide Mass Spectrometry
%0 Journal Article
%D 2008
%J ANALYTICAL CHEMISTRY
%P 7383-7391
%V 80
%N 19
%U http://dx.doi.org/10.1021/ac801096e

%A Lima T
%A Auchincloss AH
%A Coudert E
%A Keller G
%A Michoud K
%A Rivoire C
%A Bulliard V
%A de Castro E
%A Lachaize C
%A Baratin D
%A Phan I
%A Bougueleret L
%A Bairoch A
%T HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot
%0 Journal Article
%D 2008 Oct 11
%J Nucleic Acids Res
%P -
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%8 2008 Oct 11

%A Kunsoo Park
%A Joo Young Yoon
%A Sunho Lee
%A Eunok Paek
%A Heejin Park
%A Hee-Jung Jung
%A Sang-Won Lee
%T Isotopic Peak Intensity Ratio Based Algorithm for Determination of Isotopic Clusters and Monoisotopic Masses of Polypeptides from High-Resolution Mass Spectrometric Data
%0 Journal Article
%D 2008
%J ANALYTICAL CHEMISTRY
%P 7294-7303
%V 80
%N 19
%U http://dx.doi.org/10.1021/ac800913b

%A Wolfram Weckwerth
%A Sacha Baginsky
%A Klaas van Wijk
%A Joshua L. Heazlewood
%A Harvey Millar
%T The Multinational Arabidopsis Steering Subcommittee for Proteomics Assembles the Largest Proteome Database Resource for Plant Systems Biology
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 4209-4210
%V 7
%N 10
%U http://dx.doi.org/10.1021/pr800480u

%A Yoshimasa Tsuruoka
%A Jun'ichi Tsujii
%A Sophia Ananiadou
%T FACTA: a text search engine for finding associated biomedical concepts
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2559-2560
%V 24
%N 21
%U http://dx.doi.org/10.1093/bioinformatics/btn469

%A Henrik Thomas
%A Andrej Shevchenko
%T Simplified validation of borderline hits of database searches
%0 Journal Article
%D 2008
%J PROTEOMICS
%P 4173-4177
%V 8
%N 20
%U http://dx.doi.org/10.1002/pmic.200800250

%A Picotti P
%A Lam H
%A Campbell D
%A Deutsch EW
%A Mirzaei H
%A Ranish J
%A Domon B
%A Aebersold R
%T A database of mass spectrometric assays for the yeast proteome
%0 Journal Article
%D 2008
%J Nat Methods
%P 913-4
%V 5
%N 11
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18974732&dopt=Abstract

%A Darren Kessner
%A Matt Chambers
%A Robert Burke
%A David Agus
%A Parag Mallick
%T ProteoWizard: open source software for rapid proteomics tools development
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2534-2536
%V 24
%N 21
%U http://dx.doi.org/10.1093/bioinformatics/btn323