TY - JOUR A1 - Lefranc MP T1 - IMGT, the international ImMunoGeneTics information system for Immunoinformatics. Methods for querying IMGT databases, tools, and Web resources in the context of immunoinformatics JO - Methods Mol Biol Y1 - 2007 SP - 19 EP - 42 VL - 409 IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18449990&dopt=Abstract ER - TY - JOUR A1 - Yoshida Y A1 - Miyamoto M A1 - Bo X A1 - Yaoita E A1 - Yamamoto T T1 - Overview of kidney and urine proteome databases JO - Contrib Nephrol Y1 - 2008 SP - 186 EP - 97 VL - 160 IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18401170&dopt=Abstract ER - TY - JOUR A1 - Deutsch EW A1 - Lam H A1 - Aebersold R T1 - PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows JO - EMBO Rep Y1 - 2008 SP - 429 EP - 34 VL - 9 IS - 5 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18451766&dopt=Abstract ER - TY - JOUR A1 - Martens L A1 - Jones P A1 - Cote R T1 - Using the Proteomics Identifications Database (PRIDE) JO - Y1 - SP - EP - VL - IS - UR - http://dx.doi.org/10.1002/0471250953.bi1308s21 ER - TY - JOUR A1 - Park D A1 - Kim BC A1 - Cho SW A1 - Park SJ A1 - Choi JS A1 - Kim SI A1 - Bhak J A1 - Lee S T1 - MassNet: a functional annotation service for protein mass spectrometry data JO - Nucleic Acids Res Y1 - 2008/04/29 SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18448467&dopt=Abstract ER - TY - JOUR A1 - Siepen JA A1 - Belhajjame K A1 - Selley JN A1 - Embury SM A1 - Paton NW A1 - Goble CA A1 - Oliver SG A1 - Stevens R A1 - Zamboulis L A1 - Martin N A1 - Poulovassillis A A1 - Jones P A1 - Côté R A1 - Hermjakob H A1 - Pentony MM A1 - Jones DT A1 - Orengo CA A1 - Hubbard SJ T1 - ISPIDER Central: an integrated database web-server for proteomics JO - Nucleic Acids Res Y1 - 2008/04/25 SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18440977&dopt=Abstract ER - TY - JOUR A1 - Basak SC A1 - Gute BD T1 - Mathematical biodescriptors of proteomics maps: Background and applications JO - Curr Opin Drug Discov Devel Y1 - 2008 SP - 320 EP - 6 VL - 11 IS - 3 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18428085&dopt=Abstract ER - TY - JOUR A1 - Leduc RD A1 - Kelleher NL T1 - Using ProSight PTM and related tools for targeted protein identification and characterization with high mass accuracy tandem MS data JO - Y1 - SP - EP - VL - IS - UR - http://dx.doi.org/10.1002/0471250953.bi1306s19 ER - TY - JOUR A1 - Flavio Monigatti and Hanno Steen T1 - SALAMI (Spectrum ALignments Using High Accuracy Mass and HIgh Sensitivity Data): How To Make the Best out of Hybrid MS/MS Data JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 1984 EP - 1993 VL - 7 IS - 05 UR - http://dx.doi.org/10.1021/pr7006895 ER - TY - JOUR A1 - Seyfried NT A1 - Xu P A1 - Duong DM A1 - Cheng D A1 - Hanfelt J A1 - Peng J T1 - Systematic Approach for Validating the Ubiquitinated Proteome JO - Anal Chem Y1 - 2008 Apr 24 SP - EP - VL - IS - UR - http://dx.doi.org/10.1021/ac702516a ER - TY - JOUR A1 - Paolo Sonego A1 - Andras Kocsor A1 - Sandor Pongor T1 - ROC analysis: applications to the classification of biological sequences and 3D structures JO - Brief Bioinform Y1 - 2008 SP - 198 EP - 209; doi:10.1093/bib/bbm064 VL - 9 IS - 3 UR - http://bib.oxfordjournals.org/cgi/content/abstract/9/3/198?etoc ER - TY - JOUR A1 - Lacerda CM A1 - Xin L A1 - Rogers I A1 - Reardon KF T1 - Analysis of iTRAQ data using Mascot and Peaks quantification algorithms JO - Brief Funct Genomic Proteomic Y1 - 2008/04/4 SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18390580&dopt=Abstract ER - TY - JOUR A1 - Coulombe B A1 - Blanchette M A1 - Jeronimo C T1 - Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI) JO - Biochem Cell Biol Y1 - 2008 SP - 149 EP - 56 VL - 86 IS - 2 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18443628&dopt=Abstract ER - TY - JOUR A1 - Lustgarten JL A1 - Kimmel C A1 - Ryberg H A1 - Hogan W T1 - EPO-KB: A searchable knowledge base of biomarker to protein links JO - Bioinformatics Y1 - 2008/04/9 SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18400772&dopt=Abstract ER - TY - JOUR A1 - Valkenborg D A1 - Van Sanden S A1 - Lin D A1 - Kasim A A1 - Zhu Q A1 - Haldermans P A1 - Jansen I A1 - Shkedy Z A1 - Burzykowski T T1 - A cross-validation study to select a classification procedure for clinical diagnosis based on proteomic mass spectrometry JO - Y1 - SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18384267&dopt=Abstract ER - TY - JOUR A1 - Monroe ME A1 - Shaw JL A1 - Daly DS A1 - Adkins JN A1 - Smith RD T1 - MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features JO - Comput Biol Chem Y1 - 2008/02/26 SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18440872&dopt=Abstract ER - TY - JOUR A1 - Ishino Y A1 - Taniguchi H T1 - An a posteriori calibration method for improving protein identification accuracy in proteomics using electrospray ionization time-of-flight tandem mass spectrometry JO - Rapid Commun Mass Spectrom Y1 - 2008 SP - 1335 EP - 8 VL - 22 IS - 8 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18383205&dopt=Abstract ER - TY - JOUR A1 - Saha S A1 - Harrison SH A1 - Shen C A1 - Tang H A1 - Radivojac P A1 - Arnold RJ A1 - Zhang X A1 - Chen JY T1 - HIP2: An Online Database of Human Plasma Proteins from Healthy Individuals JO - Y1 - SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18439290&dopt=Abstract ER - TY - JOUR A1 - Markus Brosch A1 - Sajani Swamy A1 - Tim Hubbard A1 - Jyoti Choudhary T1 - Comparison of Mascot and X!Tandem Performance for Low and High Accuracy Mass Spectrometry and the Development of an Adjusted Mascot Threshold JO - Mol Cell Proteomics Y1 - 2008 SP - 962 EP - 970 VL - 7 IS - 5 UR - http://www.mcponline.org/cgi/content/abstract/7/5/962?etoc ER - TY - JOUR A1 - Peter A. DiMaggio A1 - Jr. A1 - Christodoulos A. Floudas A1 - Bingwen Lu A1 - John R. Yates A1 - III T1 - A Hybrid Method for Peptide Identification Using Integer Linear Optimization, Local Database Search, and Quadrupole Time-of-Flight or OrbiTrap Tandem Mass Spectrometry JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 1584 EP - 1593 VL - 7 IS - 04 UR - http://dx.doi.org/10.1021/pr700577z ER - TY - JOUR A1 - Sharmini Alagaratnam A1 - Bart J. A. Mertens A1 - Johannes C. Dalebout A1 - André M. Deelder A1 - Gert-Jan B. van Ommen A1 - Johan T. den Dunnen A1 - Peter A. C. 't Hoen T1 - Serum protein profiling in mice: Identification of Factor XIIIa as a potential biomarker for muscular dystrophy JO - PROTEOMICS Y1 - 2008 SP - 1552 EP - 1563 VL - 8 IS - 8 UR - http://dx.doi.org/10.1002/pmic.200700857 ER - TY - JOUR A1 - Zhu LR A1 - Zhang WY A1 - Yu L A1 - Zheng YH A1 - Hu J A1 - Liao QP T1 - Proteiomic patterns for endometrial cancer using SELDI-TOF-MS JO - J Zhejiang Univ Sci B Y1 - 2008 SP - 286 EP - 90 VL - 9 IS - 4 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18381802&dopt=Abstract ER - TY - JOUR A1 - Norman Pavelka A1 - Marjorie L. Fournier A1 - Selene K. Swanson A1 - Mattia Pelizzola A1 - Paola Ricciardi-Castagnoli A1 - Laurence Florens A1 - Michael P. Washburn T1 - Statistical Similarities between Transcriptomics and Quantitative Shotgun Proteomics Data JO - Mol Cell Proteomics Y1 - 2008 SP - 631 EP - 644 VL - 7 IS - 4 UR - http://www.mcponline.org/cgi/content/abstract/7/4/631?etoc ER - TY - JOUR A1 - Erik Bjorling A1 - Cecilia Lindskog A1 - Per Oksvold A1 - Jerker Linne A1 - Caroline Kampf,Sophia Hober A1 - Mathias Uhlen A1 - Fredrik Ponten T1 - A Web-based Tool for in Silico Biomarker Discovery Based on Tissue-specific Protein Profiles in Normal and Cancer Tissues JO - Mol Cell Proteomics Y1 - 2008 SP - 825 EP - 844 VL - 7 IS - 5 UR - http://www.mcponline.org/cgi/content/abstract/7/5/825?etoc ER - TY - JOUR A1 - Guo Y A1 - Yu L A1 - Wen Z A1 - Li M T1 - Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences JO - Nucleic Acids Res Y1 - 2008/04/4 SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18390576&dopt=Abstract ER - TY - JOUR A1 - Han KQ A1 - Huang G A1 - Gao CF A1 - Wang XL A1 - Ma B A1 - Sun LQ A1 - Wei ZJ T1 - Identification of lung cancer patients by serum protein profiling using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry JO - Am J Clin Oncol Y1 - 2008 SP - 133 EP - 9 VL - 31 IS - 2 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18391596&dopt=Abstract ER - TY - JOUR A1 - He Z A1 - Yang C A1 - Yu W T1 - Peak Bagging for Peptide Mass Fingerprinting JO - Bioinformatics Y1 - 2008/04/7 SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18397892&dopt=Abstract ER - TY - JOUR A1 - Myers T A1 - Law W A1 - Eng JK A1 - McIntosh M T1 - Installation and use of the Computational Proteomics Analysis System (CPAS) JO - Y1 - SP - EP - VL - IS - UR - http://dx.doi.org/10.1002/0471250953.bi1305s18 ER - TY - JOUR A1 - Kapp E A1 - Schutz F T1 - Overview of tandem mass spectrometry (MS/MS) database search algorithms JO - Y1 - SP - EP - VL - IS - UR - http://dx.doi.org/10.1002/0471140864.ps2502s49 ER - TY - JOUR A1 - Klein J A1 - Leupold S A1 - Münch R A1 - Pommerenke C A1 - Johl T A1 - Kärst U A1 - Jänsch L A1 - Jahn D A1 - Retter I T1 - ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks JO - Nucleic Acids Res Y1 - 2008/04/25 SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18440972&dopt=Abstract ER - TY - JOUR A1 - Owen W. Nadeau A1 - Gerald J. Wyckoff A1 - Justin E. Paschall A1 - Antonio Artigues A1 - Jessica Sage A1 - Maria T. Villar A1 - Gerald M. Carlson T1 - CrossSearch, a User-friendly Search Engine for Detecting Chemically Cross-linked Peptides in Conjugated Proteins JO - Mol Cell Proteomics Y1 - 2008 SP - 739 EP - 749 VL - 7 IS - 4 UR - http://www.mcponline.org/cgi/content/abstract/7/4/739?etoc ER - TY - JOUR A1 - Myriam Ferro A1 - Marianne Tardif A1 - Erwan Reguer A1 - Romain Cahuzac A1 - Christophe Bruley A1 - Thierry Vermat A1 - Estelle Nugues A1 - Marielle Vigouroux A1 - Yves Vandenbrouck A1 - Jérôme Garin A1 - Alain Viari T1 - PepLine: A Software Pipeline for High-Throughput Direct Mapping of Tandem Mass Spectrometry Data on Genomic Sequences JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 1873 EP - 1883 VL - 7 IS - 05 UR - http://dx.doi.org/10.1021/pr070415k ER - TY - JOUR A1 - Roxas BA A1 - Li Q T1 - Significance analysis of microarray for relative quantitation of LC/MS data in proteomics JO - Y1 - SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18402702&dopt=Abstract ER - TY - JOUR A1 - Alessio Ceroni A1 - Kai Maass A1 - Hildegard Geyer A1 - Rudolf Geyer A1 - Anne Dell A1 - Stuart M. Haslam T1 - GlycoWorkbench: A Tool for the Computer-Assisted Annotation of Mass Spectra of Glycans JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 1650 EP - 1659 VL - 7 IS - 04 UR - http://dx.doi.org/10.1021/pr7008252 ER - TY - JOUR A1 - Holmes MR A1 - Giddings MC T1 - Using GFS to identify encoding genomic loci from protein mass spectral data JO - Y1 - SP - EP - VL - IS - UR - http://dx.doi.org/10.1002/0471250953.bi1309s21 ER - TY - JOUR A1 - Dandass YS A1 - Burgess SC A1 - Lawrence M A1 - Bridges SM T1 - Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research JO - Y1 - SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18412963&dopt=Abstract ER - TY - JOUR A1 - Xinning Jiang A1 - Guanghui Han A1 - Shun Feng A1 - Xiaogang Jiang A1 - Mingliang Ye A1 - Xuebiao Yao A1 - Hanfa Zou T1 - Automatic Validation of Phosphopeptide Identifications by the MS2/MS3 Target-Decoy Search Strategy JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 1640 EP - 1649 VL - 7 IS - 04 UR - http://dx.doi.org/10.1021/pr700675j ER - TY - JOUR A1 - Matthew P. Campbell A1 - Louise Royle A1 - Catherine M. Radcliffe A1 - Raymond A. Dwek A1 - Pauline M. Rudd T1 - GlycoBase and autoGU: tools for HPLC-based glycan analysis JO - Bioinformatics Y1 - 2008 SP - 1214 EP - 1216 VL - 24 IS - 9 UR - http://dx.doi.org/10.1093/bioinformatics/btn090 ER - TY - JOUR A1 - Bräutigam A A1 - Shrestha RP A1 - Whitten D A1 - Wilkerson CG A1 - Carr KM A1 - Froehlich JE A1 - Weber AP T1 - 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 JO - J Biotechnol Y1 - 2008/02/17 SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18394738&dopt=Abstract ER -