%A Lefranc MP
%T IMGT, the international ImMunoGeneTics information system for Immunoinformatics. Methods for querying IMGT databases, tools, and Web resources in the context of immunoinformatics
%0 Journal Article
%D 2007
%J Methods Mol Biol
%P 19-42
%V 409
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%A Yoshida Y
%A Miyamoto M
%A Bo X
%A Yaoita E
%A Yamamoto T
%T Overview of kidney and urine proteome databases
%0 Journal Article
%D 2008
%J Contrib Nephrol
%P 186-97
%V 160
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%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18401170&dopt=Abstract

%A Deutsch EW
%A Lam H
%A Aebersold R
%T PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
%0 Journal Article
%D 2008
%J EMBO Rep
%P 429-34
%V 9
%N 5
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18451766&dopt=Abstract

%A Martens L
%A Jones P
%A Cote R
%T Using the Proteomics Identifications Database (PRIDE)
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%A Park D
%A Kim BC
%A Cho SW
%A Park SJ
%A Choi JS
%A Kim SI
%A Bhak J
%A Lee S
%T MassNet: a functional annotation service for protein mass spectrometry data
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%D 2008
%J Nucleic Acids Res
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%8 Apr 29, 2008

%A Siepen JA
%A Belhajjame K
%A Selley JN
%A Embury SM
%A Paton NW
%A Goble CA
%A Oliver SG
%A Stevens R
%A Zamboulis L
%A Martin N
%A Poulovassillis A
%A Jones P
%A Côté R
%A Hermjakob H
%A Pentony MM
%A Jones DT
%A Orengo CA
%A Hubbard SJ
%T ISPIDER Central: an integrated database web-server for proteomics
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%D 2008
%J Nucleic Acids Res
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%8 Apr 25, 2008

%A Basak SC
%A Gute BD
%T Mathematical biodescriptors of proteomics maps: Background and applications
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%D 2008
%J Curr Opin Drug Discov Devel
%P 320-6
%V 11
%N 3
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18428085&dopt=Abstract

%A Leduc RD
%A Kelleher NL
%T Using ProSight PTM and related tools for targeted protein identification and characterization with high mass accuracy tandem MS data
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%A Flavio Monigatti and Hanno Steen
%T SALAMI (Spectrum ALignments Using High Accuracy Mass and HIgh Sensitivity Data): How To Make the Best out of Hybrid MS/MS Data
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 1984-1993
%V 7
%N 05
%U http://dx.doi.org/10.1021/pr7006895

%A Seyfried NT
%A Xu P
%A Duong DM
%A Cheng D
%A Hanfelt J
%A Peng J
%T Systematic Approach for Validating the Ubiquitinated Proteome
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%D 2008 Apr 24
%J Anal Chem
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%8 2008 Apr 24

%A Paolo Sonego
%A Andras Kocsor
%A Sandor Pongor
%T ROC analysis: applications to the classification of biological sequences and 3D structures
%0 Journal Article
%D 2008
%J Brief Bioinform
%P 198-209; doi:10.1093/bib/bbm064
%V 9
%N 3
%U http://bib.oxfordjournals.org/cgi/content/abstract/9/3/198?etoc

%A Lacerda CM
%A Xin L
%A Rogers I
%A Reardon KF
%T Analysis of iTRAQ data using Mascot and Peaks quantification algorithms
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%D 2008
%J Brief Funct Genomic Proteomic
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%8 Apr 4, 2008

%A Coulombe B
%A Blanchette M
%A Jeronimo C
%T Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI)
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%D 2008
%J Biochem Cell Biol
%P 149-56
%V 86
%N 2
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18443628&dopt=Abstract

%A Lustgarten JL
%A Kimmel C
%A Ryberg H
%A Hogan W
%T EPO-KB: A searchable knowledge base of biomarker to protein links
%0 Journal Article
%D 2008
%J Bioinformatics
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%8 Apr 9, 2008

%A Valkenborg D
%A Van Sanden S
%A Lin D
%A Kasim A
%A Zhu Q
%A Haldermans P
%A Jansen I
%A Shkedy Z
%A Burzykowski T
%T A cross-validation study to select a classification procedure for clinical diagnosis based on proteomic mass spectrometry
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%A Monroe ME
%A Shaw JL
%A Daly DS
%A Adkins JN
%A Smith RD
%T MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features
%0 Journal Article
%D 2008
%J Comput Biol Chem
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%8 Feb 26, 2008

%A Ishino Y
%A Taniguchi H
%T An a posteriori calibration method for improving protein identification accuracy in proteomics using electrospray ionization time-of-flight tandem mass spectrometry
%0 Journal Article
%D 2008
%J Rapid Commun Mass Spectrom
%P 1335-8
%V 22
%N 8
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18383205&dopt=Abstract

%A Saha S
%A Harrison SH
%A Shen C
%A Tang H
%A Radivojac P
%A Arnold RJ
%A Zhang X
%A Chen JY
%T HIP2: An Online Database of Human Plasma Proteins from Healthy Individuals
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%A Markus Brosch
%A Sajani Swamy
%A Tim Hubbard
%A Jyoti Choudhary
%T Comparison of Mascot and X!Tandem Performance for Low and High Accuracy Mass Spectrometry and the Development of an Adjusted Mascot Threshold
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%D 2008
%J Mol Cell Proteomics
%P 962-970
%V 7
%N 5
%U http://www.mcponline.org/cgi/content/abstract/7/5/962?etoc

%A Peter A. DiMaggio
%A Jr.
%A Christodoulos A. Floudas
%A Bingwen Lu
%A John R. Yates
%A III
%T A Hybrid Method for Peptide Identification Using Integer Linear Optimization, Local Database Search, and Quadrupole Time-of-Flight or OrbiTrap Tandem Mass Spectrometry
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 1584-1593
%V 7
%N 04
%U http://dx.doi.org/10.1021/pr700577z

%A Sharmini Alagaratnam
%A Bart J. A. Mertens
%A Johannes C. Dalebout
%A André M. Deelder
%A Gert-Jan B. van Ommen
%A Johan T. den Dunnen
%A Peter A. C. 't Hoen
%T Serum protein profiling in mice: Identification of Factor XIIIa as a potential biomarker for muscular dystrophy
%0 Journal Article
%D 2008
%J PROTEOMICS
%P 1552-1563
%V 8
%N 8
%U http://dx.doi.org/10.1002/pmic.200700857

%A Zhu LR
%A Zhang WY
%A Yu L
%A Zheng YH
%A Hu J
%A Liao QP
%T Proteiomic patterns for endometrial cancer using SELDI-TOF-MS
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%D 2008
%J J Zhejiang Univ Sci B
%P 286-90
%V 9
%N 4
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18381802&dopt=Abstract

%A Norman Pavelka
%A Marjorie L. Fournier
%A Selene K. Swanson
%A Mattia Pelizzola
%A Paola Ricciardi-Castagnoli
%A Laurence Florens
%A Michael P. Washburn
%T Statistical Similarities between Transcriptomics and Quantitative Shotgun Proteomics Data
%0 Journal Article
%D 2008
%J Mol Cell Proteomics
%P 631-644
%V 7
%N 4
%U http://www.mcponline.org/cgi/content/abstract/7/4/631?etoc

%A Erik Bjorling
%A Cecilia Lindskog
%A Per Oksvold
%A Jerker Linne
%A Caroline Kampf,Sophia Hober
%A Mathias Uhlen
%A Fredrik Ponten
%T A Web-based Tool for in Silico Biomarker Discovery Based on Tissue-specific Protein Profiles in Normal and Cancer Tissues
%0 Journal Article
%D 2008
%J Mol Cell Proteomics
%P 825-844
%V 7
%N 5
%U http://www.mcponline.org/cgi/content/abstract/7/5/825?etoc

%A Guo Y
%A Yu L
%A Wen Z
%A Li M
%T Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences
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%J Nucleic Acids Res
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%8 Apr 4, 2008

%A Han KQ
%A Huang G
%A Gao CF
%A Wang XL
%A Ma B
%A Sun LQ
%A Wei ZJ
%T Identification of lung cancer patients by serum protein profiling using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry
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%D 2008
%J Am J Clin Oncol
%P 133-9
%V 31
%N 2
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18391596&dopt=Abstract

%A He Z
%A Yang C
%A Yu W
%T Peak Bagging for Peptide Mass Fingerprinting
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%D 2008
%J Bioinformatics
%P -
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%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18397892&dopt=Abstract
%8 Apr 7, 2008

%A Myers T
%A Law W
%A Eng JK
%A McIntosh M
%T Installation and use of the Computational Proteomics Analysis System (CPAS)
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%U http://dx.doi.org/10.1002/0471250953.bi1305s18

%A Kapp E
%A Schutz F
%T Overview of tandem mass spectrometry (MS/MS) database search algorithms
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%U http://dx.doi.org/10.1002/0471140864.ps2502s49

%A Klein J
%A Leupold S
%A Münch R
%A Pommerenke C
%A Johl T
%A Kärst U
%A Jänsch L
%A Jahn D
%A Retter I
%T ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks
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%D 2008
%J Nucleic Acids Res
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%8 Apr 25, 2008

%A Owen W. Nadeau
%A Gerald J. Wyckoff
%A Justin E. Paschall
%A Antonio Artigues
%A Jessica Sage
%A Maria T. Villar
%A Gerald M. Carlson
%T CrossSearch, a User-friendly Search Engine for Detecting Chemically Cross-linked Peptides in Conjugated Proteins
%0 Journal Article
%D 2008
%J Mol Cell Proteomics
%P 739-749
%V 7
%N 4
%U http://www.mcponline.org/cgi/content/abstract/7/4/739?etoc

%A Myriam Ferro
%A Marianne Tardif
%A Erwan Reguer
%A Romain Cahuzac
%A Christophe Bruley
%A Thierry Vermat
%A Estelle Nugues
%A Marielle Vigouroux
%A Yves Vandenbrouck
%A Jérôme Garin
%A Alain Viari
%T PepLine: A Software Pipeline for High-Throughput Direct Mapping of Tandem Mass Spectrometry Data on Genomic Sequences
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 1873-1883
%V 7
%N 05
%U http://dx.doi.org/10.1021/pr070415k

%A Roxas BA
%A Li Q
%T Significance analysis of microarray for relative quantitation of LC/MS data in proteomics
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%A Alessio Ceroni
%A Kai Maass
%A Hildegard Geyer
%A Rudolf Geyer
%A Anne Dell
%A Stuart M. Haslam
%T GlycoWorkbench: A Tool for the Computer-Assisted Annotation of Mass Spectra of Glycans
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 1650-1659
%V 7
%N 04
%U http://dx.doi.org/10.1021/pr7008252

%A Holmes MR
%A Giddings MC
%T Using GFS to identify encoding genomic loci from protein mass spectral data
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%U http://dx.doi.org/10.1002/0471250953.bi1309s21

%A Dandass YS
%A Burgess SC
%A Lawrence M
%A Bridges SM
%T Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research
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%A Xinning Jiang
%A Guanghui Han
%A Shun Feng
%A Xiaogang Jiang
%A Mingliang Ye
%A Xuebiao Yao
%A Hanfa Zou
%T Automatic Validation of Phosphopeptide Identifications by the MS2/MS3 Target-Decoy Search Strategy
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 1640-1649
%V 7
%N 04
%U http://dx.doi.org/10.1021/pr700675j

%A Matthew P. Campbell
%A Louise Royle
%A Catherine M. Radcliffe
%A Raymond A. Dwek
%A Pauline M. Rudd
%T GlycoBase and autoGU: tools for HPLC-based glycan analysis
%0 Journal Article
%D 2008
%J Bioinformatics
%P 1214-1216
%V 24
%N 9
%U http://dx.doi.org/10.1093/bioinformatics/btn090

%A Bräutigam A
%A Shrestha RP
%A Whitten D
%A Wilkerson CG
%A Carr KM
%A Froehlich JE
%A Weber AP
%T Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in non-model species: Comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes
%0 Journal Article
%D 2008
%J J Biotechnol
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%N 
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%8 Feb 17, 2008