A Data-Mining Scheme for Identifying Peptide Structural Motifs Responsible for Different MS/MS Fragmentation Intensity Patterns (Unknown)
- New search for: Huang, Yingying
- New search for: Tseng, George C.
- New search for: Yuan, Shinsheng
- New search for: Pasa-Tolic, Ljiljana
- New search for: Lipton, Mary S.
- New search for: Smith, Richard D.
- New search for: Wysocki, Vicki H.
- New search for: Huang, Yingying
- New search for: Tseng, George C.
- New search for: Yuan, Shinsheng
- New search for: Pasa-Tolic, Ljiljana
- New search for: Lipton, Mary S.
- New search for: Smith, Richard D.
- New search for: Wysocki, Vicki H.
In:
The Journal of Proteome Research
;
7
, 01
;
70-79
;
2008
- Article (Journal) / Electronic Resource
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Title:A Data-Mining Scheme for Identifying Peptide Structural Motifs Responsible for Different MS/MS Fragmentation Intensity Patterns
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Additional title:Data-Mining Scheme for Identifying Peptide Structural Motifs
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Contributors:Huang, Yingying ( author ) / Tseng, George C. ( author ) / Yuan, Shinsheng ( author ) / Pasa-Tolic, Ljiljana ( author ) / Lipton, Mary S. ( author ) / Smith, Richard D. ( author ) / Wysocki, Vicki H. ( author )
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Published in:The Journal of Proteome Research ; 7, 01 ; 70-79
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Publisher:
- New search for: American Chemical Society
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Publication date:2008-01-04
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ISSN:
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Coden:
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DOI:
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Type of media:Article (Journal)
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Type of material:Electronic Resource
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Language:Unknown
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Keywords:
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Source:
Table of contents – Volume 7, Issue 01
The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.
- 29
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Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy DatabasesKäll, Lukas / Storey, John D. / MacCoss, Michael J. / Noble, William Stafford et al. | 2008
- 35
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Modes of Inference for Evaluating the Confidence of Peptide IdentificationsFitzgibbon, Matt / Li, Qunhua / McIntosh, Martin et al. | 2008
- 40
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Posterior Error Probabilities and False Discovery Rates: Two Sides of the Same CoinKäll, Lukas / Storey, John D. / MacCoss, Michael J. / Noble, William Stafford et al. | 2008
- 45
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What’s Driving False Discovery Rates?Tabb, David L. et al. | 2008
- 47
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False Discovery Rates and Related Statistical Concepts in Mass Spectrometry-Based ProteomicsChoi, Hyungwon / Nesvizhskii, Alexey I. et al. | 2008
- 51
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An Assessment of Software Solutions for the Analysis of Mass Spectrometry Based Quantitative Proteomics DataMueller, Lukas N. / Brusniak, Mi-Youn / Mani, D. R. / Aebersold, Ruedi et al. | 2008
- 62
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High-Accuracy Peptide Mass Fingerprinting Using Peak Intensity Data with Machine LearningYang, Dongmei / Ramkissoon, Kevin / Hamlett, Eric / Giddings, Morgan C. et al. | 2008
- 70
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A Data-Mining Scheme for Identifying Peptide Structural Motifs Responsible for Different MS/MS Fragmentation Intensity PatternsHuang, Yingying / Tseng, George C. / Yuan, Shinsheng / Pasa-Tolic, Ljiljana / Lipton, Mary S. / Smith, Richard D. / Wysocki, Vicki H. et al. | 2008
- 80
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Whole Genome Searching with Shotgun Proteomic Data: Applications for Genome AnnotationSevinsky, Joel R. / Cargile, Benjamin J. / Bunger, Maureen K. / Meng, Fanyu / Yates, Nathan A. / Hendrickson, Ronald C. / Stephenson, Jr., James L. et al. | 2008
- 89
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Algorithm for Identification of Fusion Proteins via Mass SpectrometryNg, Julio / Pevzner, Pavel A. et al. | 2008
- 96
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The Standard Protein Mix Database: A Diverse Data Set To Assist in the Production of Improved Peptide and Protein Identification Software ToolsKlimek, John / Eddes, James S. / Hohmann, Laura / Jackson, Jennifer / Peterson, Amelia / Letarte, Simon / Gafken, Philip R. / Katz, Jonathan E / Mallick, Parag / Lee, Hookeun et al. | 2008
- 104
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Interactive Three-Dimensional Visualization and Contextual Analysis of Protein Interaction NetworksHo, Edwin / Webber, Richard / Wilkins, Marc R. et al. | 2008
- 113
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Clustering Millions of Tandem Mass SpectraFrank, Ari M. / Bandeira, Nuno / Shen, Zhouxin / Tanner, Stephen / Briggs, Steven P. / Smith, Richard D. / Pevzner, Pavel A. et al. | 2008
- 123
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Improving Mass Spectrometry Peak Detection Using Multiple Peak Alignment ResultsYu, Weichaun / He, Zengyou / Liu, Junfeng / Zhao, Hongyu et al. | 2008
- 130
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On the Value of Knowing a z• Ion for What It IsLiu, Jian / Liang, Xiaorong / McLuckey, Scott A. et al. | 2008
- 138
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Identification and Characterization of Disulfide Bonds in Proteins and Peptides from Tandem MS Data by Use of the MassMatrix MS/MS Search EngineXu, Hua / Zhang, Liwen / Freitas, Michael A. et al. | 2008
- 145
-
Local and Nonlocal Environments around Cis PeptidesWathen, Brent / Jia, Zongchao et al. | 2008
- 154
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In Silico Tools for Predicting Peptides Binding to HLA-Class II Molecules: More Confusion than ConclusionGowthaman, Uthaman / Agrewala, Javed N. et al. | 2008
- 164
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The Effects of Shared Peptides on Protein Quantitation in Label-Free Proteomics by LC/MS/MSJin, Shuangshuang / Daly, Donald S. / Springer, David L. / Miller, John H. et al. | 2008
- 170
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Accurate Annotation of Peptide Modifications through Unrestrictive Database SearchTanner, Stephen / Payne, Samuel H. / Dasari, Surendra / Shen, Zhouxin / Wilmarth, Phillip A. / David, Larry L. / Loomis, William F. / Briggs, Steven P. / Bafna, Vineet et al. | 2008
- 182
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Analyzing Large-Scale Proteomics Projects with Latent Semantic IndexingKlie, Sebastian / Martens, Lennart / Vizcaíno, Juan Antonio / Côté, Richard / Jones, Phil / Apweiler, Rolf / Hinneburg, Alexander / Hermjakob, Henning et al. | 2008
- 192
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Data Augmentation Algorithms for Detecting Conserved Domains in Protein Sequences: A Comparative StudyBi, Chengpeng et al. | 2008
- 202
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Deriving the Probabilities of Water Loss and Ammonia Loss for Amino Acids from Tandem Mass SpectraSun, Shiwei / Yu, Chungong / Qiao, Yantao / Lin, Yu / Dong, Gongjin / Liu, Changning / Zhang, Jingfen / Zhang, Zhuo / Cai, Jinjin / Zhang, Hong et al. | 2008
- 209
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Occurrence of Copper Proteins through the Three Domains of Life: A Bioinformatic ApproachAndreini, Claudia / Banci, Lucia / Bertini, Ivano / Rosato, Antonio et al. | 2008
- 234
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Protein Identification and Peptide Expression Resolver: Harmonizing Protein Identification with Protein Expression DataKearney, Paul / Butler, Heather / Eng, Kevin / Hugo, Patrice et al. | 2008
- 254
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Semisupervised Model-Based Validation of Peptide Identifications in Mass Spectrometry-Based ProteomicsChoi, Hyungwon / Nesvizhskii, Alexey I. et al. | 2008
- 266
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Characterization of Global Yeast Quantitative Proteome Data Generated from the Wild-Type and Glucose Repression Saccharomyces cerevisiae Strains: The Comparison of Two Quantitative MethodsUsaite, Renata / Wohlschlegel, James / Venable, John D. / Park, Sung K. / Nielsen, Jens / Olsson, Lisbeth / Yates III, John R. et al. | 2008
- 276
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Signal Detection in High-Resolution Mass Spectrometry DataMcLerran, Dale F. / Feng, Ziding / Semmes, O. John / Cazares, Lisa / Randolph, Timothy W. et al. | 2008
- 286
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Statistical Validation of Peptide Identifications in Large-Scale Proteomics Using the Target-Decoy Database Search Strategy and Flexible Mixture ModelingChoi, Hyungwon / Ghosh, Debashis / Nesvizhskii, Alexey I. et al. | 2008
- 300
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Does Trypsin Cut Before Proline?Rodriguez, Jesse / Gupta, Nitin / Smith, Richard D. / Pevzner, Pavel A. et al. | 2008
- 306
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Online Multidimensional Separation with Biphasic Monolithic Capillary Column for Shotgun Proteome AnalysisWang, Fangjun / Dong, Jing / Ye, Mingliang / Jiang, Xiaogang / Wu, Ren’an / Zou, Hanfa et al. | 2008
- 311
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Large-Scale Identification and Evolution Indexing of Tyrosine Phosphorylation Sites from Murine BrainBallif, Bryan A. / Carey, G. Richard / Sunyaev, Shamil R. / Gygi, Steven P. et al. | 2008
- 319
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Design of Recombinant Antibody Microarrays for Cell Surface Membrane ProteomicsDexlin, Linda / Ingvarsson, Johan / Frendéus, Björn / Borrebaeck, Carl A. K. / Wingren, Christer et al. | 2008
- 328
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A Quantitative Proteomic Analysis of Mitochondrial Participation in P19 Cell Neuronal DifferentiationWatkins, Jermel / Basu, Siddhartha / Bogenhagen, Daniel F. et al. | 2008
- 339
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A Proteome Resource of Ovarian Cancer Ascites: Integrated Proteomic and Bioinformatic Analyses To Identify Putative BiomarkersGortzak-Uzan, Limor / Ignatchenko, Alex / Evangelou, Andreas I. / Agochiya, Mahima / Brown, Kevin A. / St.Onge, Peter / Kireeva, Inga / Schmitt-Ulms, Gerold / Brown, Theodore J. / Murphy, Joan et al. | 2008
- 352
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Species Variation in the Fecal Metabolome Gives Insight into Differential Gastrointestinal FunctionSaric, Jasmina / Wang, Yulan / Li, Jia / Coen, Muireann / Utzinger, Jürg / Marchesi, Julian R. / Keiser, Jennifer / Veselkov, Kirill / Lindon, John C. / Nicholson, Jeremy K. et al. | 2008
- 361
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Real-Time Fluorescence Monitoring of Tryptic Digestion in ProteomicsKaruso, Peter / Crawford, Angela S. / Veal, Duncan A. / Scott, Graham B. I. / Choi, Hung-Yoon et al. | 2008
- 367
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Quantitation by Isobaric Labeling: Applications to GlycomicsAtwood, James A. / Cheng, Lei / Alvarez-Manilla, Gerardo / Warren, Nicole L. / York, William S. / Orlando, Ron et al. | 2008
- 375
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Analysis of Host-Inducing Proteome Changes in Bifidobacterium longum NCC2705 Grown in VivoYuan, Jing / Wang, Bin / Sun, Zhongke / Bo, Xin / Yuan, Xitong / He, Xiang / Zhao, Hongqing / Du, Xinying / Wang, Fang / Jiang, Zheng et al. | 2008
- 386
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Integrated Analysis of the Cerebrospinal Fluid Peptidome and ProteomeZougman, Alexandre / Pilch, Bartosz / Podtelejnikov, Alexandre / Kiehntopf, Michael / Schnabel, Claudia / Kumar, Chanchal / Mann, Matthias et al. | 2008
- 400
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Metabolomic and Proteomic Analysis of a Clonal Insulin-Producing β-Cell Line (INS-1 832/13)Fernandez, Céline / Fransson, Ulrika / Hallgard, Elna / Spégel, Peter / Holm, Cecilia / Krogh, Morten / Wårell, Kristofer / James, Peter / Mulder, Hindrik et al. | 2008
- 412
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Identification of Mouse Embryonic Stem Cell-Associated ProteinsBaharvand, Hossein / Fathi, Ali / Gourabi, Hamid / Mollamohammadi, Sepideh / Salekdeh, Ghasem Hosseini et al. | 2008
- 424
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Antiviral Phagocytosis Is Regulated by a Novel Rab-Dependent Complex in Shrimp Penaeus japonicusWu, Wenlin / Zong, Rongrong / Xu, Jianyang / Zhang, Xiaobo et al. | 2008
- 432
-
Aqueous Polymer Two-Phase Systems for the Proteomic Analysis of Plasma Membranes from Minute Brain SamplesSchindler, Jens / Lewandrowski, Urs / Sickmann, Albert / Friauf, Eckhard et al. | 2008
- 443
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Proteomic Analysis of Human Follicular Fluid Using an Alternative Bottom-Up ApproachHanrieder, Jörg / Nyakas, Adrien / Naessén, Tord / Bergquist, Jonas et al. | 2008
- 450
-
Simultaneous Analysis of Circulating Human Cytokines Using a High-Sensitivity Cytokine Biochip ArrayFitzGerald, S. Pete / McConnell, R. Ivan / Huxley, Allen et al. | 2008
- 456
-
Proteome of Murine Jejunal Brush Border Membrane VesiclesDonowitz, Mark / Singh, Siddharth / Salahuddin, Farah F. / Hogema, Boris M. / Chen, Yueping / Gucek, Marjan / Cole, Robert N. / Ham, Amy / Zachos, Nicholas C. / Kovbasnjuk, Olga et al. | 2008