TY  - JOUR
A1  - Craig D. Wagner
A1  - John T. Hall
A1  - Wendy L. White
A1  - Luke A. D. Miller
A1  - Jon D. Williams
T1  - Automated mass correction and data interpretation for protein open-access liquid chromatography-mass spectrometry
JO  - Journal of Mass Spectrometry
Y1  - 2007
SP  - 139
EP  - 149
VL  - 42
IS  - 2
UR  - http://dx.doi.org/10.1002/jms.1174
ER  - 

TY  - JOUR
A1  - Norden B
A1  - Broberg P
A1  - Lindberg C
A1  - Plymoth A
T1  - Analysis and Understanding of High-Dimensionality Data by Means of Multivariate Data Analysis
JO  - Chem Biodivers
Y1  - 2005
SP  - 1487
EP  - 1494
VL  - 2
IS  - 11
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17191948&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Orchard S
A1  - Jones P
A1  - Taylor C
A1  - Zhu W
A1  - Julian RK
A1  - Hermjakob H
A1  - Apweiler R
T1  - Proteomic data exchange and storage: the need for common standards and public repositories
JO  - Methods Mol Biol
Y1  - 2006
SP  - 261
EP  - 70
VL  - 367
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17185781&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Siepen J
A1  - Swainston N
A1  - Jones A
A1  - Hart S
A1  - Hermjakob H
A1  - Jones P
A1  - Hubbard S
T1  - An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://dx.doi.org/10.1186/1477-5956-5-4
ER  - 

TY  - JOUR
A1  - Mertens BJ
A1  - Noo ME
A1  - Tollenaar RA
A1  - Deelder AM
T1  - Mass spectrometry proteomic diagnosis: enacting the double cross-validatory paradigm
JO  - J Comput Biol
Y1  - 2006
SP  - 1591
EP  - 605
VL  - 13
IS  - 9
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17147482&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Matthiesen R
T1  - Virtual Expert Mass Spectrometrist v3.0: An Integrated Tool for Proteome Analysis
JO  - Methods Mol Biol
Y1  - 2006
SP  - 121
EP  - 38
VL  - 367
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17185773&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Eugenio Ragazzi
A1  - Salvatore Pucciarelli
A1  - Roberta Seraglia
A1  - Laura Molin
A1  - Marco Agostini
A1  - Mario Lise
A1  - Pietro Traldi
A1  - Donato Nitti
T1  - Multivariate analysis approach to the plasma protein profile of patients with advanced colorectal cancer
JO  - Journal of Mass Spectrometry
Y1  - 2006
SP  - 1546
EP  - 1553
VL  - 41
IS  - 12
UR  - http://dx.doi.org/10.1002/jms.1113
ER  - 

TY  - JOUR
A1  - Gruhler A
A1  - Matthiesen R
T1  - Quantitation with virtual expert mass spectrometrist
JO  - Methods Mol Biol
Y1  - 2006
SP  - 139
EP  - 52
VL  - 367
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17185774&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Thomsen AL
A1  - Laukens K
A1  - Matthiesen R
A1  - Jensen ON
T1  - Organization of Proteomics Data With YassDB
JO  - Methods Mol Biol
Y1  - 2006
SP  - 271
EP  - 88
VL  - 367
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17185782&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Tolmachev AV
A1  - Monroe ME
A1  - Jaitly N
A1  - Petyuk VA
A1  - Adkins JN
A1  - Smith RD
T1  - Mass measurement accuracy in analyses of highly complex mixtures based upon multidimensional recalibration
JO  - Anal Chem
Y1  - 2006
SP  - 8374
EP  - 85
VL  - 78
IS  - 24
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17165830&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Radivojac P
A1  - Iakoucheva LM
A1  - Oldfield CJ
A1  - Obradovic Z
A1  - Uversky VN
A1  - Dunker AK
T1  - Intrinsic Disorder and Functional Proteomics
JO  - Biophys J
Y1  - 2007
SP  - 1439
EP  - 56
VL  - 92
IS  - 5
UR  - http://dx.doi.org/10.1529/biophysj.106.094045
ER  - 

TY  - JOUR
A1  - Choi C
A1  - Munch R
A1  - Leupold S
A1  - Klein J
A1  - Siegel I
A1  - Thielen B
A1  - Benkert B
A1  - Kucklick M
A1  - Schobert M
A1  - Barthelmes J
A1  - Ebeling C
A1  - Haddad I
A1  - Scheer M
A1  - Grote A
A1  - Hiller K
A1  - Bunk B
A1  - Schreiber K
A1  - Retter I
A1  - Schomburg D
A1  - Jahn D
T1  - SYSTOMONAS--an integrated database for systems biology analysis of Pseudomonas
JO  - Nucl Acids Res
Y1  - 2007
SP  - D533
EP  - 7
VL  - 35
IS  - Database issue
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17202169&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Rovshan G. Sadygov
A1  - Fernando Martin Maroto
A1  - Andreas F. R. Hühmer
T1  - ChromAlign: A Two-Step Algorithmic Procedure for Time Alignment of Three-Dimensional LC-MS Chromatographic Surfaces
JO  - ANALYTICAL CHEMISTRY
Y1  - 2006
SP  - 8207
EP  - 8217
VL  - 78
IS  - 24
UR  - http://dx.doi.org/10.1021/ac060923y
ER  - 

TY  - JOUR
A1  - Bruno Meunier
A1  - Emilie Dumas
A1  - Isabelle Piec
A1  - Daniel Béchet
A1  - Michel Hébraud
A1  - Jean-François Hocquette
T1  - Assessment of Hierarchical Clustering Methodologies for Proteomic Data Mining
JO  - JOURNAL OF PROTEOME RESEARCH
Y1  - 2007
SP  - 358
EP  - 366
VL  - 6
IS  - 1
UR  - http://dx.doi.org/10.1021/pr060343h
ER  - 

TY  - JOUR
A1  - Lamesch P
A1  - Li N
A1  - Milstein S
A1  - Fan C
A1  - Hao T
A1  - Szabo G
A1  - Hu Z
A1  - Venkatesan K
A1  - Bethel G
A1  - Martin P
A1  - Rogers J
A1  - Lawlor S
A1  - McLaren S
A1  - Dricot A
A1  - Borick H
A1  - Cusick ME
A1  - Vandenhaute J
A1  - Dunham I
A1  - Hill DE
A1  - Vidal M
T1  - hORFeome v3.1: A resource of human open reading frames representing over 10,000 human genes
JO  - Genomics
Y1  - 2007
SP  - 307
EP  - 15
VL  - 89
IS  - 3
UR  - http://dx.doi.org/10.1016/j.ygeno.2006.11.012
ER  - 

TY  - JOUR
A1  - Garwood K
A1  - Garwood C
A1  - Hedeler C
A1  - Griffiths T
A1  - Swainston N
A1  - Oliver SG
A1  - Paton NW
T1  - Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17169146&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Tanner S
A1  - Shen Z
A1  - Ng J
A1  - Florea L
A1  - Guigo R
A1  - Briggs SP
A1  - Bafna V
T1  - Improving gene annotation using peptide mass spectrometry
JO  - Genome Res
Y1  - 2007
SP  - 231
EP  - 9
VL  - 17
IS  - 2
UR  - http://dx.doi.org/10.1101/gr.5646507
ER  - 

TY  - JOUR
A1  - Haibin Xu
A1  - Liming Yang
A1  - Pei Xu
A1  - Ye Tao
A1  - Zhengqiang Ma
T1  - cTrans: Generating polypeptide databases from cDNA sequences
JO  - PROTEOMICS
Y1  - 2007
SP  - 177
EP  - 179
VL  - 7
IS  - 2
UR  - http://dx.doi.org/10.1002/pmic.200600508
ER  - 

TY  - JOUR
A1  - Tekaia F
A1  - Yeramian E
T1  - Evolution of proteomes: Fundamental signatures and global trends in amino acid compositions
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17147802&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Liu J
A1  - Bell A
A1  - Bergeron J
A1  - Yanofsky C
A1  - Carrillo B
A1  - Beaudrie C
A1  - Kearney R
T1  - Methods for peptide identification by spectral comparison
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://dx.doi.org/10.1186/1477-5956-5-3
ER  - 

TY  - JOUR
A1  - Garden P
A1  - Alm R
T1  - Proteomic data exchange and storage: using proteios
JO  - Methods Mol Biol
Y1  - 2006
SP  - 241
EP  - 60
VL  - 367
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17185780&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Saito A
A1  - Nagasaki M
A1  - Oyama M
A1  - Kozuka-Hata H
A1  - Semba K
A1  - Sugano S
A1  - Yamamoto T
A1  - Miyano S
T1  - AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17233908&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Strong M
A1  - Eisenberg D
T1  - The protein network as a tool for finding novel drug targets
JO  - Prog Drug Res
Y1  - 2007
SP  - 191: 193
EP  - 215
VL  - 64
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17195476&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Mueller M
A1  - Martens L
A1  - Apweiler R
T1  - Annotating the human proteome: Beyond establishing a parts list
JO  - Biochim Biophys Acta
Y1  - 2007
SP  - 175
EP  - 91
VL  - 1774
IS  - 2
UR  - http://dx.doi.org/10.1016/j.bbapap.2006.11.011
ER  - 

TY  - JOUR
A1  - M. Reid Groseclose
A1  - Malin Andersson
A1  - William M. Hardesty
A1  - Richard M. Caprioli
T1  - Identification of proteins directly from tissue: in situ tryptic digestions coupled with imaging mass spectrometry
JO  - Journal of Mass Spectrometry
Y1  - 2007
SP  - 254
EP  - 262
VL  - 42
IS  - 2
UR  - http://dx.doi.org/10.1002/jms.1177
ER  - 

TY  - JOUR
A1  - Bergmann
A1  - Frank T.; Vallabhajosyula
A1  - Ravishankar R.; Sauro
A1  - Herbert M
T1  - Computational Tools for Modeling Protein Networks
JO  - Current Proteomics
Y1  - 2006
SP  - 181
EP  - 197
VL  - 3
IS  - 3
UR  - http://www.ingentaconnect.com/content/ben/cp/2006/00000003/00000003/art00003
ER  - 

TY  - JOUR
A1  - Verkhivker GM
T1  - Computational proteomics of biomolecular interactions in the sequence and structure space of the tyrosine kinome: Deciphering the molecular basis of the kinase inhibitors selectivity
JO  - Proteins
Y1  - 2007
SP  - 912
EP  - 29
VL  - 66
IS  - 4
UR  - http://dx.doi.org/10.1002/prot.21287
ER  - 

TY  - JOUR
A1  - Matthiesen R
T1  - Useful mass spectrometry programs freely available on the internet
JO  - Methods Mol Biol
Y1  - 2006
SP  - 303
EP  - 6
VL  - 367
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17185784&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Apatoff A
A1  - Kim E
A1  - Kliger Y
T1  - Towards alignment independent quantitative assessment of homology detection
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17205117&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Nesvizhskii AI
T1  - Protein identification by tandem mass spectrometry and sequence database searching
JO  - Methods Mol Biol
Y1  - 2006
SP  - 87
EP  - 120
VL  - 367
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17185772&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Edward L. Huttlin
A1  - Adrian D. Hegeman
A1  - Amy C. Harms
A1  - Michael R. Sussman
T1  - Prediction of Error Associated with False-Positive Rate Determination for Peptide Identification in Large-Scale Proteomics Experiments Using a Combined Reverse and Forward Peptide Sequence Database Strategy
JO  - JOURNAL OF PROTEOME RESEARCH
Y1  - 2007
SP  - 392
EP  - 398
VL  - 6
IS  - 1
UR  - http://dx.doi.org/10.1021/pr0603194
ER  - 

TY  - JOUR
A1  - Jennifer A. Siepen
A1  - Emma-Jayne Keevil
A1  - David Knight
A1  - Simon J. Hubbard
T1  - Prediction of Missed Cleavage Sites in Tryptic Peptides Aids Protein Identification in Proteomics
JO  - JOURNAL OF PROTEOME RESEARCH
Y1  - 2007
SP  - 399
EP  - 408
VL  - 6
IS  - 1
UR  - http://dx.doi.org/10.1021/pr060507u
ER  -