Search Results - "Tabb, David L"

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments by MacLean, Brendan, Tomazela, Daniela M., Shulman, Nicholas, Chambers, Matthew, Finney, Gregory L., Frewen, Barbara, Kern, Randall, Tabb, David L., Liebler, Daniel C., MacCoss, Michael J.

“…Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for…”
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Employing ProteoWizard to Convert Raw Mass Spectrometry Data by Holman, Jerry D, Tabb, David L, Mallick, Parag

“…After raw data have been captured by mass spectrometers in biological LC-MS/MS experiments, they must be converted from vendor-specific binary files to…”
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The Evolutionary Imprint of Domestication on Genome Variation and Function of the Filamentous Fungus Aspergillus oryzae by Gibbons, John G., Salichos, Leonidas, Slot, Jason C., Rinker, David C., McGary, Kriston L., King, Jonas G., Klich, Maren A., Tabb, David L., McDonald, W. Hayes, Rokas, Antonis

“…The domestication of animals, plants, and microbes fundamentally transformed the lifestyle and demography of the human species [1]. Although the genetic and…”
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Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets by Griss, Johannes, Perez-Riverol, Yasset, Lewis, Steve, Tabb, David L, Dianes, José A, del-Toro, Noemi, Rurik, Marc, Walzer, Mathias, Kohlbacher, Oliver, Hermjakob, Henning, Wang, Rui, Vizcaíno, Juan Antonio

“…A newly developed algorithm enabled clustering of all 256 million (66 million identified and 190 million unidentified) peptide MS/MS spectra available in the…”
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MyriMatch:  Highly Accurate Tandem Mass Spectral Peptide Identification by Multivariate Hypergeometric Analysis by Tabb, David L, Fernando, Christopher G, Chambers, Matthew C

“…Shotgun proteomics experiments are dependent upon database search engines to identify peptides from tandem mass spectra. Many of these algorithms score…”
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MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets by Potgieter, Matthys G, Nel, Andrew J M, Fortuin, Suereta, Garnett, Shaun, Wendoh, Jerome M, Tabb, David L, Mulder, Nicola J, Blackburn, Jonathan M

“…Microbiome research is providing important new insights into the metabolic interactions of complex microbial ecosystems involved in fields as diverse as the…”
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A Face in the Crowd: Recognizing Peptides Through Database Search by Eng, Jimmy K., Searle, Brian C., Clauser, Karl R., Tabb, David L.

“…Peptide identification via tandem mass spectrometry sequence database searching is a key method in the array of tools available to the proteomics researcher…”
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Proteomic Parsimony through Bipartite Graph Analysis Improves Accuracy and Transparency by Zhang, Bing, Chambers, Matthew C, Tabb, David L

“…Assembling peptides identified from LC−MS/MS spectra into a list of proteins is a critical step in analyzing shotgun proteomics data. As one peptide sequence…”
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Proteomics Standards Initiative: Fifteen Years of Progress and Future Work by Deutsch, Eric W, Orchard, Sandra, Binz, Pierre-Alain, Bittremieux, Wout, Eisenacher, Martin, Hermjakob, Henning, Kawano, Shin, Lam, Henry, Mayer, Gerhard, Menschaert, Gerben, Perez-Riverol, Yasset, Salek, Reza M, Tabb, David L, Tenzer, Stefan, Vizcaíno, Juan Antonio, Walzer, Mathias, Jones, Andrew R

“…The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software…”
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Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work by Deutsch, Eric W., Vizcaíno, Juan Antonio, Jones, Andrew R., Binz, Pierre-Alain, Lam, Henry, Klein, Joshua, Bittremieux, Wout, Perez-Riverol, Yasset, Tabb, David L., Walzer, Mathias, Ricard-Blum, Sylvie, Hermjakob, Henning, Neumann, Steffen, Mak, Tytus D., Kawano, Shin, Mendoza, Luis, Van Den Bossche, Tim, Gabriels, Ralf, Bandeira, Nuno, Carver, Jeremy, Pullman, Benjamin, Sun, Zhi, Hoffmann, Nils, Shofstahl, Jim, Zhu, Yunping, Licata, Luana, Quaglia, Federica, Tosatto, Silvio C. E., Orchard, Sandra E.

“…The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled…”
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Comparative Proteomics Analysis between Maize and Sorghum Uncovers Important Proteins and Metabolic Pathways Mediating Drought Tolerance by Ali, Ali Elnaeim Elbasheir, Husselmann, Lizex Hollenbach, Tabb, David L, Ludidi, Ndiko

“…Drought severely affects crop yield and yield stability. Maize and sorghum are major crops in Africa and globally, and both are negatively impacted by drought…”
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Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data by Wang, Xiaojing, Slebos, Robbert J. C, Wang, Dong, Halvey, Patrick J, Tabb, David L, Liebler, Daniel C, Zhang, Bing

“…The standard shotgun proteomics data analysis strategy relies on searching MS/MS spectra against a context-independent protein sequence database derived from…”
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SWATH-MS based proteomic profiling of pancreatic ductal adenocarcinoma tumours reveals the interplay between the extracellular matrix and related intracellular pathways by Nweke, Ekene Emmanuel, Naicker, Previn, Aron, Shaun, Stoychev, Stoyan, Devar, John, Tabb, David L, Omoshoro-Jones, Jones, Smith, Martin, Candy, Geoffrey

“…Pancreatic cancer accounts for 2.8% of new cancer cases worldwide and is projected to become the second leading cause of cancer-related deaths by 2030…”
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The Human Proteome Organization–Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry by Bittremieux, Wout, Walzer, Mathias, Tenzer, Stefan, Zhu, Weimin, Salek, Reza M, Eisenacher, Martin, Tabb, David L

“…To have confidence in results acquired during biological mass spectrometry experiments, a systematic approach to quality control is of vital importance…”
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enterocyte microvillus is a vesicle-generating organelle by McConnell, Russell E, Higginbotham, James N, Shifrin, David A. Jr, Tabb, David L, Coffey, Robert J, Tyska, Matthew J

“…For decades, enterocyte brush border microvilli have been viewed as passive cytoskeletal scaffolds that serve to increase apical membrane surface area…”
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Proteomic Analysis of Chinese Hamster Ovary Cells by Baycin-Hizal, Deniz, Tabb, David L, Chaerkady, Raghothama, Chen, Lily, Lewis, Nathan E, Nagarajan, Harish, Sarkaria, Vishaldeep, Kumar, Amit, Wolozny, Daniel, Colao, Joe, Jacobson, Elena, Tian, Yuan, O’Meally, Robert N, Krag, Sharon S, Cole, Robert N, Palsson, Bernhard O, Zhang, Hui, Betenbaugh, Michael

“…To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular…”
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Greazy: Open-Source Software for Automated Phospholipid Tandem Mass Spectrometry Identification by Kochen, Michael A, Chambers, Matthew C, Holman, Jay D, Nesvizhskii, Alexey I, Weintraub, Susan T, Belisle, John T, Islam, M. Nurul, Griss, Johannes, Tabb, David L

“…Lipid identification from data produced with high-throughput technologies is essential to the elucidation of the roles played by lipids in cellular function…”
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DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics by Tabb, David L, McDonald, W Hayes, Yates, 3rd, John R

“…The components of complex peptide mixtures can be separated by liquid chromatography, fragmented by tandem mass spectrometry, and identified by the SEQUEST…”
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Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer by Woo, Sunghee, Cha, Seong Won, Bonissone, Stefano, Na, Seungjin, Tabb, David L, Pevzner, Pavel A, Bafna, Vineet

“…Aiming toward an improved understanding of the regulation of proteins in cancer, recent studies from the Clinical Proteomic Tumor Analysis Consortium (CPTAC)…”
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proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data by Wang, Xiaojing, Slebos, Robbert J.C., Chambers, Matthew C., Tabb, David L., Liebler, Daniel C., Zhang, Bing

“…To facilitate genome-based representation and analysis of proteomics data, we developed a new bioinformatics framework, proBAMsuite, in which a central…”
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