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SPS' DigestIssue 53, 22-Jul-2008 |
Matching isotopic distributions from metabolically labeled samples
Sean McIlwain, David Page, Edward L. Huttlin, and Michael R. Sussman
Bioinformatics (2008) 24(13): i339-i347
A Computational Strategy to Analyze Label-Free Temporal Bottom-Up Proteomics Data
Xiuxia Du, Stephen J. Callister, Nathan P. Manes, Joshua N. Adkins, Roxana A. Alexandridis, Xiaohua Zeng, Jung Hyeob Roh, William E. Smith, Timothy J. Donohue, Samuel Kaplan, Richard D. Smith, and Mary S. Lipton
JOURNAL OF PROTEOME RESEARCH (2008) 7(07): 2595-2604
High-performance hardware implementation of a parallel database search engine for real-time peptide mass fingerprinting
Istvan A. Bogdan, Jenny Rivers, Robert J. Beynon, and Daniel Coca
Bioinformatics (2008) 24(13): 1498-1502
PhosphoScan: A Probability-Based Method for Phosphorylation Site Prediction Using MS2/MS3 Pair Information
Yunhu Wan, Diane Cripps, Stefani Thomas, Patricia Campbell, Nicholas Ambulos, Ting Chen, and Austin Yang
JOURNAL OF PROTEOME RESEARCH (2008) 7(07): 2803-2811
Logical Analysis of Data (LAD) model for the early diagnosis of acute ischemic stroke
Reddy A, Wang H, Yu H, Bonates TO, Gulabani V, Azok J, Hoehn G, Hammer PL, Baird AE, Li KC.
BMC Med Inform Decis Mak (2008) 8(1): 30
Data standards and controlled vocabularies for proteomics
Martens L, Palazzi LM, Hermjakob H.
Methods Mol Biol (2008) 484: 279-86
MIAPEGelDB, a web-based submission tool and public repository for MIAPE gel electrophoresis documents
Xavier Robin, Christine Hoogland, Ron D. Appel, Frédérique Lisacek
Journal of Proteomics (2008) 71(2): 249-251
Detection of co-eluted peptides using database search methods
Alves G, Ogurtsov AY, Kwok S, Wu WW, Wang G, Shen RF, Yu YK.
Biol Direct (2008) 3(1): 27
PhosphoScore: An Open-Source Phosphorylation Site Assignment Tool for MSn Data
Brian E. Ruttenberg, Trairak Pisitkun, Mark A. Knepper, and Jason D. Hoffert
JOURNAL OF PROTEOME RESEARCH (2008) 7(07): 3054-3059
DAnTE: a statistical tool for quantitative analysis of -omics data
Ashoka D. Polpitiya, Wei-Jun Qian, Navdeep Jaitly, Vladislav A. Petyuk, Joshua N. Adkins, David G. Camp, II, Gordon A. Anderson, and Richard D. Smith
Bioinformatics (2008) 24(13): 1556-1558
On E-values for tandem MS scoring schemes
Mark R. Segal
Bioinformatics (2008) 24(14): 1652-1653
The PRIDE Proteomics Identifications Database: Data Submission, Query, and Dataset Comparison
Jones P, Côté R.
Methods Mol Biol (2008) 484: 287-303
Proteomic analysis of amniotic fluid to identify women with preterm labor and intra-amniotic inflammation/infection: The use of a novel computational method to analyze mass spectrometric profiling
Romero R, Espinoza J, Rogers WT, Moser A, Kae Nien J, Pedro Kusanovic J, Gotsch F, Erez O, Gomez R, Edwin S, Hassan SS.
J Matern Fetal Neonatal Med (2008) 21(6): 367-87
Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology
Lin CY, Chin CH, Wu HH, Chen SH, Ho CW, Ko MT.
Nucl Acids Res (2008) 36(Web Server issue): W438-43
An accurate and efficient algorithm for Peptide and ptm identification by tandem mass spectrometry
Ning K, Ng HK, Leong HW.
Genome Inform (2007) 19: 119-30
Monte Carlo Simulation-Based Algorithms for Analysis of Shotgun Proteomic Data
Hua Xu and Michael A. Freitas
JOURNAL OF PROTEOME RESEARCH (2008) 7(07): 2605-2615
A Bayesian estimator of protein-protein association probabilities
Jason M. Gilmore, Deanna L. Auberry, Julia L. Sharp, Amanda M. White, Kevin K. Anderson, and Don S. Daly
Bioinformatics (2008) 24(13): 1554-1555
Classification of premalignant pancreatic cancer mass-spectrometry data using decision tree ensembles
Ge G, Wong GW.
BMC Bioinformatics (2008) 9(1): 275
Comprehensive Comparison of Collision Induced Dissociation and Electron Transfer Dissociation
Henrik Molina, Rune Matthiesen, Kumaran Kandasamy, and Akhilesh Pandey
ANALYTICAL CHEMISTRY (2008) 80(13): 4825-4835
PRINCESS, a Protein Interaction Confidence Evaluation System with Multiple Data Sources
Dong Li, Wanlin Liu, Zhongyang Liu, Jian Wang, Qijun Liu, Yunping Zhu, and Fuchu He
Mol Cell Proteomics (2008) 7(6): 1043-1052
Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments
Kosaku Shinoda, Masaru Tomita, and Yasushi Ishihama
Bioinformatics (2008) 24(14): 1590-1595
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
Bobbie-Jo M. Webb-Robertson, William R. Cannon, Christopher S. Oehmen, Anuj R. Shah, Vidhya Gurumoorthi, Mary S. Lipton, and Katrina M. Waters
Bioinformatics (2008) 24(13): 1503-1509
Rapid and Accurate Peptide Identification from Tandem Mass Spectra
Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael J. MacCoss, and William S. Noble
JOURNAL OF PROTEOME RESEARCH (2008) 7(07): 3022-3027
OMSSAGUI: An open-source user interface component to configure and run the OMSSA search engine
Ravi Tharakan, Lennart Martens, Jennifer E. Van Eyk, David R. Graham
PROTEOMICS (2008) 8(12): 2376-2378
In response to 'On E-value for tandem MS scoring schemes'
Jainab Khatun and Morgan Giddings
Bioinformatics (2008) 24(14): 1654
Ovarian cancer diagnosis with complementary learning fuzzy neural network
Tan TZ, Quek C, Ng GS, Razvi K.
Artif Intell Med (2008) 43(3): 207-22
On preprocessing and antisymmetry in de novo Peptide sequencing: improving efficiency and accuracy
Ning K, Ye N, Leong HW.
J Bioinform Comput Biol (2008) 6(3): 467-92
Validation of Endogenous Peptide Identifications Using a Database of Tandem Mass Spectra
Maria Fälth, Marcus Svensson, Anna Nilsson, Karl Sköld, David Fenyö, and Per E. Andren
JOURNAL OF PROTEOME RESEARCH (2008) 7(07): 3049-3053
Properties of Average Score Distributions of SEQUEST: The Probability Ratio Method
Salvador Martinez-Bartolome, Pedro Navarro, Fernando Martin-Maroto, Daniel Lopez-Ferrer, Antonio Ramos-Fernandez, Margarita Villar, Josefa P. Garcia-Ruiz, and Jesus Vazquez
Mol Cell Proteomics (2008) 7(6): 1135-1145
Postexperiment Monoisotopic Mass Filtering and Refinement (PE-MMR) of Tandem Mass Spectrometric Data Increases Accuracy of Peptide Identification in LC/MS/MS
Byunghee Shin, Hee-Jung Jung, Seok-Won Hyung, Hokeun Kim, Dongkyu Lee, Cheolju Lee, Myeong-Hee Yu, and Sang-Won Lee
Mol Cell Proteomics (2008) 7(6): 1124-1134
High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example
de Souza GA, Malen H, Softeland T, Salensminde G, Prasad S, Jonassen I, Wiker HG.
BMC Genomics (2008) 9(1): 316
Quantitative Analysis of Isotope Distributions In Proteomic Mass Spectrometry Using Least-Squares Fourier Transform Convolution
Edit Sperling, Anne E. Bunner, Michael T. Sykes, and James R. Williamson
ANALYTICAL CHEMISTRY (2008) 80(13): 4906-4917
The zebrafish secretome
Klee EW.
Zebrafish (2008) 5(2): 131-8
PepSeeker: Mining Information from Proteomic Data
Siepen JA, Selley JN, Hubbard SJ.
Methods Mol Biol (2008) 484: 319-32
Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseases
Pattin KA, Moore JH.
Hum Genet Early Edition: published 13-Jun-2008
Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification
Aaron A. Klammer, Sheila M. Reynolds, Jeff A. Bilmes, Michael J. MacCoss, and William Stafford Noble
Bioinformatics (2008) 24(13): i348-i356
A central resource for platelet proteomics
Cagney G, McRedmond J.
Arterioscler Thromb Vasc Biol (2008) 28(7): 1214-5
Evaluation of the Variables Characterized by Significant Discriminating Power in the Application of SIMCA Classification Method to Proteomic Studies
Emilio Marengo, Elisa Robotti, Marco Bobba, and Pier Giorgio Righetti
JOURNAL OF PROTEOME RESEARCH (2008) 7(07): 2789-2796
Isotope correction of mass spectrometry profiles
Günther Eibl, Katussevani Bernardo, Therese Koal, Steven L. Ramsay, Klaus M. Weinberger, Armin Graber
Rapid Communications in Mass Spectrometry (2008) 22(14): 2248-2252
LIMS and the art of MS proteomics
Piggee C
Anal Chem (2008) 80(13): 4801-6
Toward High-Throughput and Reliable Peptide Identification via MS/MS Spectra
Liu J.
Methods Mol Biol (2008) 484: 333-44
TOPDOM: database of domains and motifs with conservative location in transmembrane proteins
Gabor E. Tusnady, Lajos Kalmar, Hedi Hegyi, Peter Tompa, and Istvan Simon
Bioinformatics (2008) 24(12): 1469-1470
The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server
Christine Hoogland, Khaled Mostaguir, Ron D. Appel, Frédérique Lisacek
Journal of Proteomics (2008) 71(2): 245-248
SjTPdb: integrated transcriptome and proteome database and analysis platform for Schistosoma japonicum
Liu F, Chen P, Cui SJ, Wang ZQ, Han ZG.
BMC Genomics (2008) 9(1): 304
Wavelet-Based Method for Noise Characterization and Rejection in High-Performance Liquid Chromatography Coupled to Mass Spectrometry
Salvatore Cappadona, Fredrik Levander, Maria Jansson, Peter James, Sergio Cerutti, and Linda Pattini
ANALYTICAL CHEMISTRY (2008) 80(13): 4960-4968
Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis
Ashley Vaughan, Sum-Ying Chiu, Gowthaman Ramasamy, Ling Li, Malcolm J. Gardner, Alice S. Tarun, Stefan H.I. Kappe, and Xinxia Peng
Bioinformatics (2008) 24(13): i383-i389
Comparison of Drug Distribution Images from Whole-Body Thin Tissue Sections Obtained Using Desorption Electrospray Ionization Tandem Mass Spectrometry and Autoradiography
Vilmos Kertesz, Gary J. Van Berkel, Marissa Vavrek, Kenneth A. Koeplinger, Bradley B. Schneider, and Thomas R. Covey
ANALYTICAL CHEMISTRY (2008) 80(13): 5168-5177
Reversible jump MCMC approach for peak identification for stroke SELDI mass spectrometry using mixture model
Yuan Wang, Xiaobo Zhou, Honghui Wang, King Li, Lixiu Yao, and Stephen T.C. Wong
Bioinformatics (2008) 24(13): i407-i413
The Expression of Heat Shock Protein HSP60A Reveals a Dynamic Mitochondrial Pattern in Drosophila melanogaster Embryos
Luis Alberto Baena-López, Jana Alonso, Javier Rodriguez, and Juan F. Santarén
JOURNAL OF PROTEOME RESEARCH (2008) 7(07): 2780-2788
Toward a Full Characterization of the Human 20S Proteasome Subunits and Their Isoforms by a Combination of Proteomic Approaches
Uttenweiler-Joseph S, Claverol S, Sylvius L, Bousquet-Dubouch MP, Burlet-Schiltz O, Monsarrat B.
Methods Mol Biol (2008) 484: 111-30
The zebrafish secretome
Klee EW.
Zebrafish (2008) 5(2): 131-8
Proteomes of the aphid Macrosiphum euphorbiae in its resistance and susceptibility responses to differently compatible parasitoids
Nguyen TT, Boudreault S, Michaud D, Cloutier C.
Insect Biochem Mol Biol (2008) 38(7): 730-9
Plasmodium lipid rafts contain proteins implicated in vesicular trafficking and signalling as well as members of the PIR superfamily, potentially implicated in host immune system interactions
Francesco Di Girolamo, Carla Raggi, Cecilia Birago, Elisabetta Pizzi, Marco Lalle, Leonardo Picci, Tomasino Pace, Angela Bachi, Joke de Jong, Chris J. Janse, Andrew P. Waters, Massimo Sargiacomo, Marta Ponzi
PROTEOMICS (2008) 8(12): 2500-2513
Current developments on Schistosoma proteomics
Verjovski-Almeida S, Demarco R.
Acta Trop Early Edition: published 1-May-2008
Evolutionary and Transcriptional Analysis of Karyopherin {beta} Superfamily Proteins
Yu Quan, Zhi-Liang Ji, Xiao Wang, Alan M. Tartakoff, and Tao Tao
Mol Cell Proteomics (2008) 7(7): 1254-1269
From genome to proteome: great progress in the domesticated silkworm(Bombyx mori L.)
Zhou Z, Yang H, Zhong B.
Acta Biochim Biophys Sin (Shanghai) (2008) 40(7): 601-11
Identification of Glucose-Derived Cross-Linking Sites in Ribonuclease A
Zhenyu Dai, Benlian Wang, Gang Sun, Xingjun Fan, Vernon E. Anderson, and Vincent M. Monnier
JOURNAL OF PROTEOME RESEARCH (2008) 7(07): 2756-2768
Rho-GDI{alpha} Downregulated by Low Shear Stress Promotes Vascular Smooth Muscle Cell Migration and Apoptosis: A Proteomic Analysis
Qi YX, Qu MJ, Long DK, Liu B, Yao QP, Chien S, Jiang ZL.
Cardiovasc Res Early Edition: published 7-Jun-2008
Multiple Phosphorylations in the C-terminal Tail of Plant Plasma Membrane Aquaporins: Role in Subcellular Trafficking of AtPIP2;1 in Response to Salt Stress
Sodana Prak, Sonia Hem, Julie Boudet, Gaelle Viennois, Nicolas Sommerer, Michel Rossignol, Christophe Maurel, and Veronique Santoni
Mol Cell Proteomics (2008) 7(6): 1019-1030
Comparative proteomics of chloroplasts envelopes from C3 and C4 plants reveals specific adaptations of the plastid envelope to C4 photosynthesis and candidate proteins required for maintaining C4 metabolite fluxes
Brautigam A, Hofmann-Benning S, Weber AP.
Plant Physiol Early Edition: published 3-Jul-2008
CRHR1-dependent effects on protein expression and posttranslational modification in AtT-20 cells
Kronsbein HC, Jastorff AM, Maccarrone G, Stalla G, Wurst W, Holsboer F, Turck CW, Deussing JM.
Mol Cell Endocrinol Early Edition: published 5-Jun-2008
A Proteomic Profiling Approach to Reveal a Novel Role of BnD22 (Brassica napus drought 22 kD)/Water Soluble Chlorophyll binding Protein in young leaves during Nitrogen Remobilization induced by Stressful conditions
Desclos M, Dubousset L, Etienne P, Caherec FL, Satoh H, Bonnefoy J, Ourry A, Avice JC.
Plant Physiol Early Edition: published 13-Jun-2008
Evolutionary expansion and anatomical specialization of synapse proteome complexity
Emes RD, Pocklington AJ, Anderson CN, Bayes A, Collins MO, Vickers CA, Croning MD, Malik BR, Choudhary JS, Armstrong JD, Grant SG.
Nat Neurosci (2008) 11(7): 799-806
The in Vivo Phosphorylation Sites in Multiple Isoforms of Amphiphysin I from Rat Brain Nerve Terminals
George E. Craft, Mark E. Graham, Nicolai Bache, Martin R. Larsen, and Phillip J. Robinson
Mol Cell Proteomics (2008) 7(6): 1146-1161
Large Scale Screening for Novel Rab Effectors Reveals Unexpected Broad Rab Binding Specificity
Mitsunori Fukuda, Eiko Kanno, Koutaro Ishibashi, and Takashi Itoh
Mol Cell Proteomics (2008) 7(6): 1031-1042
Scaled-Down Purification Protocol To Access Proteomic Analysis of 20S Proteasome from Human Tissue Samples: Comparison of Normal and Tumor Colorectal Cells
Manuelle Ducoux-Petit, Sandrine Uttenweiler-Joseph, Franck Brichory, Marie-Pierre Bousquet-Dubouch, Odile Burlet-Schiltz, Jean-François Haeuw, and Bernard Monsarrat
JOURNAL OF PROTEOME RESEARCH (2008) 7(07): 2852-2859
Effect of Environmental Stress during Grain Filling on the Soluble Proteome of Wheat (Triticum aestivum) Dough Liquor
Sancho AI, Gillabert M, Tapp H, Shewry PR, Skeggs PK, Mills EN.
J Agric Food Chem (2008) 56(13): 5386-93
Trypanosoma brucei Mitochondrial Ribosomes: Affinity Purification and Component Identification by Mass Spectrometry
Alena Zikova, Aswini K. Panigrahi, Rachel A. Dalley, Nathalie Acestor, Atashi Anupama, Yuko Ogata, Peter J. Myler, and Kenneth Stuart
Mol Cell Proteomics (2008) 7(7): 1286-1296
In-Depth Investigation of Soybean Seed-Filling Proteome and Comparison with a Parallel Study of Rapeseed
Agrawal GK, Hajduch M, Graham K, Thelen JJ.
Plant Physiol Early Edition: published 3-Jul-2008
Proteomic Analysis of the Retinal Rod Outer Segment Disks
Isabella Panfoli, Luca Musante, Angela Bachi, Silvia Ravera, Daniela Calzia, Angela Cattaneo, Maurizio Bruschi, Paolo Bianchini, Alberto Diaspro, Alessandro Morelli, Isidoro M. Pepe, Carlo Tacchetti, and Giovanni Candiano
JOURNAL OF PROTEOME RESEARCH (2008) 7(07): 2654-2669
Electrophoretic Analysis of the Mitochondrial Outer Membrane Rupture Induced by Permeability Transition
Hans Zischka, Nathanael Larochette, Florian Hoffmann, Daniela Hamöller, Nora Jägemann, Josef Lichtmannegger, Luise Jennen, Josef Müller-Höcker, Frigga Roggel, Martin Göttlicher, Angelika M. Vollmar, and Guido Kroemer
ANALYTICAL CHEMISTRY (2008) 80(13): 5051-5058
The recovery of Mycobacterium avium subspecies paratuberculosis from the intestine of infected ruminants for proteomic evaluation
Egan S, Lanigan M, Shiell B, Beddome G, Stewart D, Vaughan J, Michalski WP.
J Microbiol Methods Early Edition: published 14-May-2008
Grape berry plasma membrane proteome analysis and its differential expression during ripening
Zhang J, Ma H, Feng J, Zeng L, Wang Z, Chen S.
J Exp Bot Early Edition: published 11-Jun-2008
DsbA plays a critical and multi-faceted role in the production of secreted virulence factors by the phytopathogen, Erwinia carotovora subsp. atroseptica
Coulthurst SJ, Lilley KS, Hedley PE, Liu H, Toth IK, Salmond GP.
J Biol Chem Early Edition: published 18-Jun-2008