%A Shao C
%A Sun W
%A Li F
%A Yang R
%A Zhang L
%A Gao Y
%T Oscore: a combined score to reduce false negative rates for peptide identification in tandem mass spectrometry analysis
%0 Journal Article
%D 2008
%J J Mass Spectrom
%P -
%V 
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18698557&dopt=Abstract
%8 Aug 12, 2008

%A Bingwen Lu
%A Cristian I. Ruse
%A John R. Yates III
%T Colander: A Probability-Based Support Vector Machine Algorithm for Automatic Screening for CID Spectra of Phosphopeptides Prior to Database Search
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 3628-3634
%V 7
%N 08
%U http://dx.doi.org/10.1021/pr8001194

%A Olivier Filangi
%A Yoann Beausse
%A Anthony Assi
%A Ludovic Legrand
%A Jean-Marc Larre
%A Veronique Martin
%A Olivier Collin
%A Christophe Caron
%A Hugues Leroy
%A David Allouche
%T BioMAJ: a flexible framework for databanks synchronization and processing
%0 Journal Article
%D 2008
%J Bioinformatics
%P 1823-1825
%V 24
%N 16
%U http://dx.doi.org/10.1093/bioinformatics/btn325

%A Eric Deutsch
%T mzML: A single, unifying data format for mass spectrometer output
%0 Journal Article
%D 2008
%J PROTEOMICS
%P 2776-2777
%V 8
%N 14
%U http://dx.doi.org/10.1002/pmic.200890049

%A Junqueira M
%A Spirin V
%A Balbuena TS
%A Thomas H
%A Adzhubei I
%A Sunyaev S
%A Shevchenko A
%T Protein identification pipeline for the homology-driven proteomics
%0 Journal Article
%D 2008
%J J Proteomics
%P 346-56
%V 71
%N 3
%U http://dx.doi.org/10.1016/j.jprot.2008.07.003

%A Alexander Scherl
%A Yihsuan Shannon Tsai
%A Scott A. Shaffer
%A David R. Goodlett
%T Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses
%0 Journal Article
%D 2008
%J PROTEOMICS
%P 2791-2797
%V 8
%N 14
%U http://dx.doi.org/10.1002/pmic.200800045

%A Lisa Berglund
%A Erik Björling
%A Kalle Jonasson
%A Johan Rockberg
%A Linn Fagerberg
%A Cristina Al-Khalili Szigyarto
%A Åsa Sivertsson
%A Mathias Uhlén
%T A whole-genome bioinformatics approach to selection of antigens for systematic antibody generation
%0 Journal Article
%D 2008
%J PROTEOMICS
%P 2832-2839
%V 8
%N 14
%U http://dx.doi.org/10.1002/pmic.200800203

%A Louis Ramaley
%A Lisandra Cubero Herrera
%T Software for the calculation of isotope patterns in tandem mass spectrometry
%0 Journal Article
%D 2008
%J Rapid Communications in Mass Spectrometry
%P 2707-2714
%V 22
%N 17
%U http://dx.doi.org/10.1002/rcm.3668

%A A.M. Willemsen
%A G.A. Jansen
%A J.C. Komen
%A S. van Hooff
%A H.R. Waterham
%A P.M.T. Brites
%A R.J.A. Wanders
%A A.H.C. van Kampen
%T Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways
%0 Journal Article
%D 2008
%J Bioinformatics
%P i21-i27
%V 24
%N 16
%U http://dx.doi.org/10.1093/bioinformatics/btn274

%A Duncan P. Brown
%T Efficient functional clustering of protein sequences using the Dirichlet process
%0 Journal Article
%D 2008
%J Bioinformatics
%P 1765-1771
%V 24
%N 16
%U http://dx.doi.org/10.1093/bioinformatics/btn244

%A Louie B
%A Tarczy-Hornoch P
%A Higdon R
%A Kolker E
%T Validating Annotations for Uncharacterized Proteins in Shewanella oneidensis
%0 Journal Article
%D 2008
%J OMICS
%P -
%V 
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18687039&dopt=Abstract
%8 Aug 7, 2008

%A Sebastian Bocker and Florian Rasche
%T Towards de novo identification of metabolites by analyzing tandem mass spectra
%0 Journal Article
%D 2008
%J Bioinformatics
%P i49-i55
%V 24
%N 16
%U http://dx.doi.org/10.1093/bioinformatics/btn270

%A Julia E. Bandow
%A John D. Baker
%A Matthias Berth
%A Cory Painter
%A Osvaldo J. Sepulveda
%A Kelly A. Clark
%A Iain Kilty
%A Ruth A. VanBogelen
%T Improved image analysis workflow for 2-D gels enables large-scale 2-D gel-based proteomics studies - COPD biomarker discovery study
%0 Journal Article
%D 2008
%J PROTEOMICS
%P 3030-3041
%V 8
%N 15
%U http://dx.doi.org/10.1002/pmic.200701184

%A Chia-Ying Yang
%A Chao-Hui Chang
%A Ya-Ling Yu
%A Tsu-Chun Emma Lin
%A Sheng-An Lee
%A Chueh-Chuan Yen
%A Jinn-Moon Yang
%A Jin-Mei Lai
%A Yi-Ren Hong
%A Tzu-Ling Tseng
%A Kun-Mao Chao
%A Chi-Ying F. Huang
%T PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database
%0 Journal Article
%D 2008
%J Bioinformatics
%P i14-i20
%V 24
%N 16
%U http://dx.doi.org/10.1093/bioinformatics/btn297

%A Yaniv Loewenstein and Michal Linial
%T Connect the dots: exposing hidden protein family connections from the entire sequence tree
%0 Journal Article
%D 2008
%J Bioinformatics
%P i193-i199
%V 24
%N 16
%U http://dx.doi.org/10.1093/bioinformatics/btn301

%A Kosuke Hashimoto
%A Ichigaku Takigawa
%A Motoki Shiga
%A Minoru Kanehisa
%A Hiroshi Mamitsuka
%T Mining significant tree patterns in carbohydrate sugar chains
%0 Journal Article
%D 2008
%J Bioinformatics
%P i167-i173
%V 24
%N 16
%U http://dx.doi.org/10.1093/bioinformatics/btn293

%A Predrag Radivojac
%A Peter H. Baenziger
%A Maricel G. Kann
%A Matthew E. Mort
%A Matthew W. Hahn
%A Sean D. Mooney
%T Gain and loss of phosphorylation sites in human cancer
%0 Journal Article
%D 2008
%J Bioinformatics
%P i241-i247
%V 24
%N 16
%U http://dx.doi.org/10.1093/bioinformatics/btn267

%A Gammerman A
%A Nouretdinov I
%A Burford B
%A Chervonenkis A
%A Vovk V
%A Luo Z
%T Clinical mass spectrometry proteomic diagnosis by conformal predictors
%0 Journal Article
%D 
%J 
%P -
%V 
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18673293&dopt=Abstract

%A Jardin-Mathe O
%A Bonnel D
%A Franck J
%A Wisztorski M
%A Macagno E
%A Fournier I
%A Salzet M
%T MITICS (MALDI Imaging Team Imaging Computing System): A new open source mass spectrometry imaging software
%0 Journal Article
%D 2008
%J J Proteomics
%P 332-45
%V 71
%N 3
%U http://dx.doi.org/10.1016/j.jprot.2008.07.004

%A Jung Hun Oh
%A Young Bun Kim
%A Prem Gurnani
%A Kevin P. Rosenblatt
%A Jean X. Gao
%T Biomarker selection and sample prediction for multi-category disease on MALDI-TOF data
%0 Journal Article
%D 2008
%J Bioinformatics
%P 1812-1818
%V 24
%N 16
%U http://dx.doi.org/10.1093/bioinformatics/btn316

%A Deukwoo Kwon
%A Marina Vannucci
%A Joon Jin Song
%A Jaesik Jeong
%A Ruth M. Pfeiffer
%T A novel wavelet-based thresholding method for the pre-processing of mass spectrometry data that accounts for heterogeneous noise
%0 Journal Article
%D 2008
%J PROTEOMICS
%P 3019-3029
%V 8
%N 15
%U http://dx.doi.org/10.1002/pmic.200701010

%A Andreas Quandt
%A Patricia Hernandez
%A Alexandre Masselot
%A Celine Hernandez
%A Sergio Maffioletti
%A Cesare Pautasso
%A Ron D. Appel
%A Frederique Lisacek
%T swissPIT: a novel approach for pipelined analysis of mass spectrometry data
%0 Journal Article
%D 2008
%J Bioinformatics
%P 1416-1417
%V 24
%N 11
%U http://dx.doi.org/10.1093/bioinformatics/btn139

%A Samuel H. Payne
%A Margaret Yau
%A Marcus B. Smolka
%A Stephen Tanner
%A Huilin Zhou
%A Vineet Bafna
%T Phosphorylation-Specific MS/MS Scoring for Rapid and Accurate Phosphoproteome Analysis
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 3373-3381
%V 7
%N 08
%U http://dx.doi.org/10.1021/pr800129m

%A Matthiesen R
%A Jensen ON
%T Analysis of mass spectrometry data in proteomics
%0 Journal Article
%D 2008
%J Methods Mol Biol
%P 105-22
%V 453
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18712299&dopt=Abstract

%A Goffard N
%A Weiller G
%T Identifying components of complexes
%0 Journal Article
%D 2008
%J Methods Mol Biol
%P 257-65
%V 453
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18712308&dopt=Abstract

%A Aleksandr Morgulis
%A George Coulouris
%A Yan Raytselis
%A Thomas L. Madden
%A Richa Agarwala
%A Alejandro A. Schaffer
%T Database indexing for production MegaBLAST searches
%0 Journal Article
%D 2008
%J Bioinformatics
%P 1757-1764
%V 24
%N 16
%U http://dx.doi.org/10.1093/bioinformatics/btn322

%A Kristoffer Forslund and Erik L. L. Sonnhammer
%T Predicting protein function from domain content
%0 Journal Article
%D 2008
%J Bioinformatics
%P 1681-1687
%V 24
%N 15
%U http://dx.doi.org/10.1093/bioinformatics/btn312

%A Jayesh Pandey
%A Mehmet Koyuturk
%A Shankar Subramaniam
%A Ananth Grama
%T Functional coherence in domain interaction networks
%0 Journal Article
%D 2008
%J Bioinformatics
%P i28-i34
%V 24
%N 16
%U http://dx.doi.org/10.1093/bioinformatics/btn296

%A Claus Lundegaard
%A Ole Lund
%A Morten Nielsen
%T Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers
%0 Journal Article
%D 2008
%J Bioinformatics
%P 1397-1398
%V 24
%N 11
%U http://dx.doi.org/10.1093/bioinformatics/btn128

%A Benjamin J. Cargile
%A Joel R. Sevinsky
%A Amal S. Essader
%A Jerry P. Eu
%A James L. Stephenson Jr
%T Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects
%0 Journal Article
%D 2008
%J ELECTROPHORESIS
%P 2768-2778
%V 29
%N 13
%U http://dx.doi.org/10.1002/elps.200700701

%A Aude Martinez
%A José A. Traverso
%A Benoît Valot
%A Myriam Ferro
%A Christelle Espagne
%A Geneviève Ephritikhine
%A Michel Zivy
%A Carmela Giglione
%A Thierry Meinnel
%T Extent of N-terminal modifications in cytosolic proteins from eukaryotes
%0 Journal Article
%D 2008
%J PROTEOMICS
%P 2809-2831
%V 8
%N 14
%U http://dx.doi.org/10.1002/pmic.200701191

%A Gelio Alves
%A Wells W. Wu
%A Guanghui Wang
%A Rong-Fong Shen
%A Yi-Kuo Yu
%T Enhancing Peptide Identification Confidence by Combining Search Methods
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 3102-3113
%V 7
%N 08
%U http://dx.doi.org/10.1021/pr700798h

%A Maclean D
%A Burrell MA
%A Studholme DJ
%A Jones AM
%T PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data
%0 Journal Article
%D 
%J 
%P -
%V 
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18710483&dopt=Abstract

%A A. D. J. van Dijk
%A D. Bosch
%A C. J. F. ter Braak
%A A. R. van der Krol
%A R. C. H. J. van Ham
%T Predicting sub-Golgi localization of type II membrane proteins
%0 Journal Article
%D 2008
%J Bioinformatics
%P 1779-1786
%V 24
%N 16
%U http://dx.doi.org/10.1093/bioinformatics/btn309

%A Magno Junqueira
%A Victor Spirin
%A Tiago Santana Balbuena
%A Patrice Waridel
%A Vineeth Surendranath
%A Grigoriy Kryukov
%A Ivan Adzhubei
%A Henrik Thomas
%A Shamil Sunyaev
%A Andrej Shevchenko
%T Separating the Wheat from the Chaff: Unbiased Filtering of Background Tandem Mass Spectra Improves Protein Identification
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 3382-3395
%V 7
%N 08
%U http://dx.doi.org/10.1021/pr800140v

%A Sven-Eric Schelhorn
%A Thomas Lengauer
%A Mario Albrecht
%T An integrative approach for predicting interactions of protein regions
%0 Journal Article
%D 2008
%J Bioinformatics
%P i35-i41
%V 24
%N 16
%U http://dx.doi.org/10.1093/bioinformatics/btn290

%A Sangtae Kim
%A Nitin Gupta
%A Pavel A. Pevzner
%T Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 3354-3363
%V 7
%N 08
%U http://dx.doi.org/10.1021/pr8001244

%A Lukas Kall
%A John D. Storey
%A William Stafford Noble
%T Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry
%0 Journal Article
%D 2008
%J Bioinformatics
%P i42-i48
%V 24
%N 16
%U http://dx.doi.org/10.1093/bioinformatics/btn294

%A Hongzhan H
%A Shukla HD
%A Cathy W
%A Satya S
%T Challenges and solutions in proteomics
%0 Journal Article
%D 2007
%J Curr Genomics
%P 21-8
%V 8
%N 1
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18645629&dopt=Abstract

%A Takashi Ishida and Kengo Kinoshita
%T Prediction of disordered regions in proteins based on the meta approach
%0 Journal Article
%D 2008
%J Bioinformatics
%P 1344-1348
%V 24
%N 11
%U http://dx.doi.org/10.1093/bioinformatics/btn195