TY - JOUR A1 - Craig D. Wenger A1 - Michael T. Boyne II A1 - Jonathan T. Ferguson A1 - Dana E. Robinson A1 - Neil L. Kelleher T1 - Versatile Online−Offline Engine for Automated Acquisition of High-Resolution Tandem Mass Spectra JO - ANALYTICAL CHEMISTRY Y1 - 2008 SP - 8055 EP - 8063 VL - 80 IS - 21 UR - http://dx.doi.org/10.1021/ac8010704 ER - TY - JOUR A1 - Bringans S A1 - Kendrick TS A1 - Lui J A1 - Lipscombe R T1 - A comparative study of the accuracy of several de novo sequencing software packages for datasets derived by matrix-assisted laser desorption/ionisation and electrospray JO - Rapid Commun Mass Spectrom Y1 - 2008 SP - 3450 EP - 3454 VL - 22 IS - 21 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18837480&dopt=Abstract ER - TY - JOUR A1 - Hammami R A1 - Ben Hamida J A1 - Vergoten G A1 - Fliss I T1 - PhytAMP: a database dedicated to antimicrobial plant peptides JO - Nucleic Acids Res Y1 - 2008/10/4 SP - EP - VL - IS - UR - http://dx.doi.org/10.1093/nar/gkn655 ER - TY - JOUR A1 - Sun Q A1 - Zybailov B A1 - Majeran W A1 - Friso G A1 - Olinares PD A1 - van Wijk KJ T1 - PPDB, the Plant Proteomics Database at Cornell JO - Nucleic Acids Res Y1 - 2008/10/2 SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18832363&dopt=Abstract ER - TY - JOUR A1 - Wolfgang Hoehenwarter A1 - Joost T. van Dongen A1 - Stefanie Wienkoop A1 - Matthias Steinfath A1 - Jan Hummel A1 - Alexander Erban A1 - Ronan Sulpice A1 - Babette Regierer A1 - Joachim Kopka A1 - Peter Geigenberger A1 - Wolfram Weckwerth T1 - A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment JO - PROTEOMICS Y1 - 2008 SP - 4214 EP - 4225 VL - 8 IS - 20 UR - http://dx.doi.org/10.1002/pmic.200701047 ER - TY - JOUR A1 - Hendrickson EL A1 - Lamont RJ A1 - Hackett M T1 - Tools for Interpreting Large-scale Protein Profiling in Microbiology JO - J Dent Res Y1 - 2008 SP - 1004 EP - 15 VL - 87 IS - 11 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18946006&dopt=Abstract ER - TY - JOUR A1 - Chatr-aryamontri A A1 - Kerrien S A1 - Khadake J A1 - Orchard S A1 - Ceol A A1 - Licata L A1 - Castagnoli L A1 - Costa S A1 - Derow C A1 - Huntley R A1 - Aranda B A1 - Leroy C A1 - Thorneycroft D A1 - Apweiler R A1 - Cesareni G A1 - Hermjakob H T1 - MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data JO - Y1 - SP - EP - VL - IS - UR - http://dx.doi.org/10.1186/gb-2008-9-s2-s5 ER - TY - JOUR A1 - Swaney DL A1 - McAlister GC A1 - Coon JJ T1 - Decision tree-driven tandem mass spectrometry for shotgun proteomics JO - Nat Methods Y1 - 2008 SP - 959 EP - 64 VL - 5 IS - 11 UR - http://dx.doi.org/10.1038/nmeth.1260 ER - TY - JOUR A1 - Tonikian R A1 - Zhang Y A1 - Sazinsky SL A1 - Currell B A1 - Yeh JH A1 - Reva B A1 - Held HA A1 - Appleton BA A1 - Evangelista M A1 - Wu Y A1 - Xin X A1 - Chan AC A1 - Seshagiri S A1 - Lasky LA A1 - Sander C A1 - Boone C A1 - Bader GD A1 - Sidhu SS T1 - A specificity map for the PDZ domain family JO - Y1 - SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18828675&dopt=Abstract ER - TY - JOUR A1 - Ahrens CH A1 - Brunner E A1 - Hafen E A1 - Aebersold R A1 - Basler K T1 - A proteome catalog of Drosophila melanogaster: an essential resource for targeted quantitative proteomics JO - Fly (Austin) Y1 - 2007 SP - 182 EP - 6 VL - 1 IS - 3 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18820430&dopt=Abstract ER - TY - JOUR A1 - Monsellier E A1 - Ramazzotti M A1 - Taddei N A1 - Chiti F T1 - Aggregation propensity of the human proteome JO - Y1 - SP - EP - VL - IS - UR - http://dx.doi.org/10.1371/journal.pcbi.1000199 ER - TY - JOUR A1 - Poh-Kuan Chong A1 - Huiyin Lee A1 - Jacklyn Wai-Fun Kong A1 - Marie Chiew-Shia Loh A1 - Chee-Hong Wong A1 - Yoon-Pin Lim T1 - Phosphoproteomics, oncogenic signaling and cancer research JO - PROTEOMICS Y1 - 2008 SP - 4370 EP - 4382 VL - 8 IS - 21 UR - http://dx.doi.org/10.1002/pmic.200800051 ER - TY - JOUR A1 - Gnad F A1 - Oroshi M A1 - Birney E A1 - Mann M T1 - MAPU 2.0: high-accuracy proteomes mapped to genomes JO - Nucleic Acids Res Y1 - 2008/10/23 SP - EP - VL - IS - UR - http://dx.doi.org/10.1093/nar/gkn773 ER - TY - JOUR A1 - Andrew R. Jones and Sandra Orchard T1 - Minimum Reporting Guidelines for Proteomics Released by the Proteomics Standards Initiative JO - Mol Cell Proteomics Y1 - 2008 SP - 2067 EP - 2068 VL - 7 IS - 10 UR - http://www.mcponline.org/cgi/content/full/7/10/2067?etoc ER - TY - JOUR A1 - Haleh Safavi A1 - Nicolle Correa A1 - Wei Xiong A1 - Anindya Roy A1 - Tülay Adali A1 - Valeriy R. Korostyshevskiy A1 - Carol C. Whisnant A1 - Françoise Seillier-Moiseiwitsch T1 - Independent component analysis of 2-D electrophoresis gels JO - ELECTROPHORESIS Y1 - 2008 SP - 4017 EP - 4026 VL - 29 IS - 19 UR - http://dx.doi.org/10.1002/elps.200800028 ER - TY - JOUR A1 - Jimmy K. Eng A1 - Bernd Fischer A1 - Jonas Grossmann A1 - Michael J. MacCoss T1 - A Fast SEQUEST Cross Correlation Algorithm JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 4598 EP - 4602 VL - 7 IS - 10 UR - http://dx.doi.org/10.1021/pr800420s ER - TY - JOUR A1 - Candong Wei A1 - Junping Peng A1 - Zhaohui Xiong A1 - Jian Yang A1 - Jing Wang A1 - Qi Jin T1 - Subproteomic tools to increase genome annotation complexity JO - PROTEOMICS Y1 - 2008 SP - 4209 EP - 4213 VL - 8 IS - 20 UR - http://dx.doi.org/10.1002/pmic.200800226 ER - TY - JOUR A1 - Kandasamy K A1 - Keerthikumar S A1 - Goel R A1 - Mathivanan S A1 - Patankar N A1 - Shafreen B A1 - Renuse S A1 - Pawar H A1 - Ramachandra YL A1 - Acharya PK A1 - Ranganathan P A1 - Chaerkady R A1 - Prasad TS A1 - Pandey A T1 - Human Proteinpedia: a unified discovery resource for proteomics research JO - Nucleic Acids Res Y1 - 2008/10/23 SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18948298&dopt=Abstract ER - TY - JOUR A1 - Ali R. Vaezzadeh A1 - Céline Hernandez A1 - Oscar Vadas A1 - Jacques J. M. Deshusses A1 - Pierre Lescuyer A1 - Frédérique Lisacek A1 - Denis F. Hochstrasser T1 - pICarver: A Software Tool and Strategy for Peptides Isoelectric Focusing JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 4336 EP - 4345 VL - 7 IS - 10 UR - http://dx.doi.org/10.1021/pr8002672 ER - TY - JOUR A1 - Erik Bjorling and Mathias Uhlen T1 - Antibodypedia, a Portal for Sharing Antibody and Antigen Validation Data JO - Mol Cell Proteomics Y1 - 2008 SP - 2028 EP - 2037 VL - 7 IS - 10 UR - http://www.mcponline.org/cgi/content/abstract/7/10/2028?etoc ER - TY - JOUR A1 - Lisa Berglund A1 - Erik Bjorling A1 - Per Oksvold A1 - Linn Fagerberg A1 - Anna Asplund A1 - Cristina Al-Khalili Szigyarto A1 - Anja Persson A1 - Jenny Ottosson A1 - Henrik Wernerus A1 - Peter Nilsson A1 - Emma Lundberg A1 - Asa Sivertsson A1 - Sanjay Navani A1 - Kenneth Wester A1 - Caroline Kampf A1 - Sophia Hobe T1 - A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies JO - Mol Cell Proteomics Y1 - 2008 SP - 2019 EP - 2027 VL - 7 IS - 10 UR - http://www.mcponline.org/cgi/content/abstract/7/10/2019?etoc ER - TY - JOUR A1 - Xia Cao and Alexey I. Nesvizhskii T1 - Improved Sequence Tag Generation Method for Peptide Identification in Tandem Mass Spectrometry JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 4422 EP - 4434 VL - 7 IS - 10 UR - http://dx.doi.org/10.1021/pr800400q ER - TY - JOUR A1 - The UniProt Consortium T1 - The Universal Protein Resource (UniProt) 2009 JO - Nucleic Acids Res Y1 - 2008/10/4 SP - EP - VL - IS - UR - http://dx.doi.org/10.1093/nar/gkn664 ER - TY - JOUR A1 - Jian Liu A1 - Alexandre Erassov A1 - Patrick Halina A1 - Myra Canete A1 - Nguyen Dinh Vo A1 - Clement Chung A1 - Gerard Cagney A1 - Alexandr Ignatchenko A1 - Vincent Fong A1 - Andrew Emili T1 - Sequential Interval Motif Search: Unrestricted Database Surveys of Global MS/MS Data Sets for Detection of Putative Post-Translational Modifications JO - ANALYTICAL CHEMISTRY Y1 - 2008 SP - 7846 EP - 7854 VL - 80 IS - 20 UR - http://dx.doi.org/10.1021/ac8009017 ER - TY - JOUR A1 - XiaoChun Xu A1 - Dong Yu A1 - Wei Fang A1 - Yushao Cheng A1 - Ziliang Qian A1 - WenCong Lu A1 - Yudong Cai A1 - Kaiyan Feng T1 - Prediction of Peptidase Category Based on Functional Domain Composition JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 4521 EP - 4524 VL - 7 IS - 10 UR - http://dx.doi.org/10.1021/pr800292w ER - TY - JOUR A1 - Suresh Mathivanan and Akhilesh Pandey T1 - Human Proteinpedia as a Resource for Clinical Proteomics JO - Mol Cell Proteomics Y1 - 2008 SP - 2038 EP - 2047 VL - 7 IS - 10 UR - http://www.mcponline.org/cgi/content/abstract/7/10/2038?etoc ER - TY - JOUR A1 - Rodríguez-Pérez MA A1 - Medina-Aunon A A1 - Encarnación-Guevara SM A1 - Bernal-Silvia S A1 - Barrera-Saldaña H A1 - Albar-Ramírez JP T1 - In silico analysis of protein neoplastic biomarkers for cervix and uterine cancer JO - Clin Transl Oncol Y1 - 2008 SP - 604 EP - 17 VL - 10 IS - 10 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18940741&dopt=Abstract ER - TY - JOUR A1 - Xudong Yao A1 - Pamela Diego A1 - Alexis A. Ramos A1 - Yu Shi T1 - Averagine-Scaling Analysis and Fragment Ion Mass Defect Labeling in Peptide Mass Spectrometry JO - ANALYTICAL CHEMISTRY Y1 - 2008 SP - 7383 EP - 7391 VL - 80 IS - 19 UR - http://dx.doi.org/10.1021/ac801096e ER - TY - JOUR A1 - Lima T A1 - Auchincloss AH A1 - Coudert E A1 - Keller G A1 - Michoud K A1 - Rivoire C A1 - Bulliard V A1 - de Castro E A1 - Lachaize C A1 - Baratin D A1 - Phan I A1 - Bougueleret L A1 - Bairoch A T1 - HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot JO - Nucleic Acids Res Y1 - 2008 Oct 11 SP - EP - VL - IS - UR - http://dx.doi.org/10.1093/nar/gkn661 ER - TY - JOUR A1 - Kunsoo Park A1 - Joo Young Yoon A1 - Sunho Lee A1 - Eunok Paek A1 - Heejin Park A1 - Hee-Jung Jung A1 - Sang-Won Lee T1 - Isotopic Peak Intensity Ratio Based Algorithm for Determination of Isotopic Clusters and Monoisotopic Masses of Polypeptides from High-Resolution Mass Spectrometric Data JO - ANALYTICAL CHEMISTRY Y1 - 2008 SP - 7294 EP - 7303 VL - 80 IS - 19 UR - http://dx.doi.org/10.1021/ac800913b ER - TY - JOUR A1 - Wolfram Weckwerth A1 - Sacha Baginsky A1 - Klaas van Wijk A1 - Joshua L. Heazlewood A1 - Harvey Millar T1 - The Multinational Arabidopsis Steering Subcommittee for Proteomics Assembles the Largest Proteome Database Resource for Plant Systems Biology JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 4209 EP - 4210 VL - 7 IS - 10 UR - http://dx.doi.org/10.1021/pr800480u ER - TY - JOUR A1 - Yoshimasa Tsuruoka A1 - Jun'ichi Tsujii A1 - Sophia Ananiadou T1 - FACTA: a text search engine for finding associated biomedical concepts JO - Bioinformatics Y1 - 2008 SP - 2559 EP - 2560 VL - 24 IS - 21 UR - http://dx.doi.org/10.1093/bioinformatics/btn469 ER - TY - JOUR A1 - Henrik Thomas A1 - Andrej Shevchenko T1 - Simplified validation of borderline hits of database searches JO - PROTEOMICS Y1 - 2008 SP - 4173 EP - 4177 VL - 8 IS - 20 UR - http://dx.doi.org/10.1002/pmic.200800250 ER - TY - JOUR A1 - Picotti P A1 - Lam H A1 - Campbell D A1 - Deutsch EW A1 - Mirzaei H A1 - Ranish J A1 - Domon B A1 - Aebersold R T1 - A database of mass spectrometric assays for the yeast proteome JO - Nat Methods Y1 - 2008 SP - 913 EP - 4 VL - 5 IS - 11 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18974732&dopt=Abstract ER - TY - JOUR A1 - Darren Kessner A1 - Matt Chambers A1 - Robert Burke A1 - David Agus A1 - Parag Mallick T1 - ProteoWizard: open source software for rapid proteomics tools development JO - Bioinformatics Y1 - 2008 SP - 2534 EP - 2536 VL - 24 IS - 21 UR - http://dx.doi.org/10.1093/bioinformatics/btn323 ER -