Search Results - "Seymour, Sean L."

Nonlinear Fitting Method for Determining Local False Discovery Rates from Decoy Database Searches by Tang, Wilfred H, Shilov, Ignat V, Seymour, Sean L

“…False discovery rate (FDR) analyses of protein and peptide identification results using decoy database searching conventionally report aggregate or global FDRs…”
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The Paragon Algorithm, a Next Generation Search Engine That Uses Sequence Temperature Values and Feature Probabilities to Identify Peptides from Tandem Mass Spectra by Shilov, Ignat V., Seymour, Sean L., Patel, Alpesh A., Loboda, Alex, Tang, Wilfred H., Keating, Sean P., Hunter, Christie L., Nuwaysir, Lydia M., Schaeffer, Daniel A.

“…The Paragon™ Algorithm, a novel database search engine for the identification of peptides from tandem mass spectrometry data, is presented. Sequence…”
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The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results by Jones, Andrew R., Eisenacher, Martin, Mayer, Gerhard, Kohlbacher, Oliver, Siepen, Jennifer, Hubbard, Simon J., Selley, Julian N., Searle, Brian C., Shofstahl, James, Seymour, Sean L., Julian, Randall, Binz, Pierre-Alain, Deutsch, Eric W., Hermjakob, Henning, Reisinger, Florian, Griss, Johannes, Vizcaíno, Juan Antonio, Chambers, Matthew, Pizarro, Angel, Creasy, David

“…We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by the Proteomics Standards Initiative. The…”
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Proteomics Standards Initiative Extended FASTA Format by Binz, Pierre-Alain, Shofstahl, Jim, Vizcaíno, Juan Antonio, Barsnes, Harald, Chalkley, Robert J, Menschaert, Gerben, Alpi, Emanuele, Clauser, Karl, Eng, Jimmy K, Lane, Lydie, Seymour, Sean L, Sánchez, Luis Francisco Hernández, Mayer, Gerhard, Eisenacher, Martin, Perez-Riverol, Yasset, Kapp, Eugene A, Mendoza, Luis, Baker, Peter R, Collins, Andrew, Van Den Bossche, Tim, Deutsch, Eric W

“…Mass-spectrometry-based proteomics enables the high-throughput identification and quantification of proteins, including sequence variants and…”
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The PSI-MOD community standard for representation of protein modification data by Garavelli, John S, Montecchi-Palazzi, Luisa, Beavis, Ron, Binz, Pierre-Alain, Chalkley, Robert J, Cottrell, John, Creasy, David, Shofstahl, Jim, Seymour, Sean L

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Guidelines for reporting the use of mass spectrometry informatics in proteomics by Taylor, Chris F, Vandenbrouck, Yves, Barkovich, Robert, Seymour, Sean L, Julian, Randall K, Binz, Pierre-Alain, Creasy, David, Horn, David M, Beavis, Ronald C

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Workflow for analysis of high mass accuracy salivary data set using MaxQuant and ProteinPilot search algorithm by Jagtap, Pratik, Bandhakavi, Sricharan, Higgins, LeeAnn, McGowan, Thomas, Sa, Rongxiao, Stone, Matthew D., Chilton, John, Arriaga, Edgar A., Seymour, Sean L., Griffin, Timothy J.

“…LTQ Orbitrap data analyzed with ProteinPilot can be further improved by MaxQuant raw data processing, which utilizes precursor‐level high mass accuracy data…”
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A cross-platform toolkit for mass spectrometry and proteomics by Chambers, Matthew C, Maclean, Brendan, Burke, Robert, Amodei, Dario, Ruderman, Daniel L, Neumann, Steffen, Gatto, Laurent, Fischer, Bernd, Pratt, Brian, Egertson, Jarrett, Hoff, Katherine, Kessner, Darren, Tasman, Natalie, Shulman, Nicholas, Frewen, Barbara, Baker, Tahmina A, Brusniak, Mi-Youn, Paulse, Christopher, Creasy, David, Flashner, Lisa, Kani, Kian, Moulding, Chris, Seymour, Sean L, Nuwaysir, Lydia M, Lefebvre, Brent, Kuhlmann, Frank, Roark, Joe, Rainer, Paape, Detlev, Suckau, Hemenway, Tina, Huhmer, Andreas, Langridge, James, Connolly, Brian, Chadick, Trey, Holly, Krisztina, Eckels, Josh, Deutsch, Eric W, Moritz, Robert L, Katz, Jonathan E, Agus, David B, MacCoss, Michael, Tabb, David L, Mallick, Parag

“…Mass-spectrometry-based proteomics has become an important component of biological research. Numerous proteomics methods have been developed to identify and…”
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A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies by Jagtap, Pratik, Goslinga, Jill, Kooren, Joel A., McGowan, Thomas, Wroblewski, Matthew S., Seymour, Sean L., Griffin, Timothy J.

“…Large databases (>106 sequences) used in metaproteomic and proteogenomic studies present challenges in matching peptide sequences to MS/MS data using…”
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systems view of epithelial-mesenchymal transition signaling states by Thomson, Stuart, Petti, Filippo, Sujka-Kwok, Izabela, Mercado, Peter, Bean, James, Monaghan, Melissa, Seymour, Sean L, Argast, Gretchen M, Epstein, David M, Haley, John D

“…Epithelial-mesenchymal transition (EMT) is an important contributor to the invasion and metastasis of epithelial-derived cancers. While considerable effort has…”
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CysTRAQ — A combination of iTRAQ and enrichment of cysteinyl peptides for uncovering and quantifying hidden proteomes by Tambor, Vojtech, Hunter, Christie L., Seymour, Sean L., Kacerovsky, Marian, Stulik, Jiri, Lenco, Juraj

“…Shotgun proteomics is capable of characterizing differences in both protein quality and quantity, and has been applied in various biomedical applications…”
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A standardized framing for reporting protein identifications in mzIdentML 1.2 by Seymour, Sean L., Farrah, Terry, Binz, Pierre-Alain, Chalkley, Robert J., Cottrell, John S., Searle, Brian C., Tabb, David L., Vizcaíno, Juan Antonio, Prieto, Gorka, Uszkoreit, Julian, Eisenacher, Martin, Martínez-Bartolomé, Salvador, Ghali, Fawaz, Jones, Andrew R.

“…Inferring which protein species have been detected in bottom‐up proteomics experiments has been a challenging problem for which solutions have been maturing…”
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Guidelines for reporting the use of mass spectrometry in proteomics by Taylor, Chris F, Lilley, Kathryn, Resing, Kathryn, Hühmer, Andreas, Macht, Marcus, Raso, Roberto, Aebersold, Ruedi, Müller, Dieter, Neubert, Thomas A, Nickson, Janice, Binz, Pierre-Alain, Tsugita, Akira, Zeng, Rong, Affolter, Michel, Xenarios, Ioannis, Julian, Randall K, Seymour, Sean L, Deutsch, Eric W, Kussmann, Martin, Mann, Matthias, Patterson, Scott D, Barkovich, Robert, Horn, David M

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Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles) by Kinsinger, Christopher R, Apffel, James, Baker, Mark, Bian, Xiaopeng, Borchers, Christoph H, Bradshaw, Ralph, Brusniak, Mi-Youn, Chan, Daniel W, Deutsch, Eric W, Domon, Bruno, Gorman, Jeff, Grimm, Rudolf, Hancock, William, Hermjakob, Henning, Horn, David, Hunter, Christie, Kolar, Patrik, Kraus, Hans-Joachim, Langen, Hanno, Linding, Rune, Moritz, Robert L, Omenn, Gilbert S, Orlando, Ron, Pandey, Akhilesh, Ping, Peipei, Rahbar, Amir, Rivers, Robert, Seymour, Sean L, Simpson, Richard J, Slotta, Douglas, Smith, Richard D, Stein, Stephen E, Tabb, David L, Tagle, Danilo, Yates, John R, Rodriguez, Henry

“…Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking…”
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Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles) by Kinsinger, Christopher R., Apffel, James, Baker, Mark, Bian, Xiaopeng, Borchers, Christoph H., Bradshaw, Ralph, Brusniak, Mi-Youn, Chan, Daniel W., Deutsch, Eric W., Domon, Bruno, Gorman, Jeff, Grimm, Rudolf, Hancock, William, Hermjakob, Henning, Horn, David, Hunter, Christie, Kolar, Patrik, Kraus, Hans-Joachim, Langen, Hanno, Linding, Rune, Moritz, Robert L., Omenn, Gilbert S., Orlando, Ron, Pandey, Akhilesh, Ping, Peipei, Rahbar, Amir, Rivers, Robert, Seymour, Sean L., Simpson, Richard J., Slotta, Douglas, Smith, Richard D., Stein, Stephen E., Tabb, David L., Tagle, Danilo, Yates, John R., Rodriguez, Henry

“…Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking…”
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Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles) by Kinsinger, Christopher R., Apffel, James, Baker, Mark, Bian, Xiaopeng, Borchers, Christoph H., Bradshaw, Ralph, Brusniak, Mi-Youn, Chan, Daniel W., Deutsch, Eric W., Domon, Bruno, Gorman, Jeff, Grimm, Rudolf, Hancock, William, Hermjakob, Henning, Horn, David, Hunter, Christie, Kolar, Patrik, Kraus, Hans-Joachim, Langen, Hanno, Linding, Rune, Moritz, Robert L., Omenn, Gilbert S., Orlando, Ron, Pandey, Akhilesh, Ping, Peipei, Rahbar, Amir, Rivers, Robert, Seymour, Sean L., Simpson, Richard J., Slotta, Douglas, Smith, Richard D., Stein, Stephen E., Tabb, David L., Tagle, Danilo, Yates, John R., Rodriguez, Henry

“…Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking…”
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Workflow for analysis of high mass accuracy salivary data set using M ax Q uant and P rotein P ilot search algorithm by Jagtap, Pratik, Bandhakavi, Sricharan, Higgins, LeeAnn, McGowan, Thomas, Sa, Rongxiao, Stone, Matthew D., Chilton, John, Arriaga, Edgar A., Seymour, Sean L., Griffin, Timothy J.

“…LTQ O rbitrap data analyzed with P rotein P ilot can be further improved by M ax Q uant raw data processing, which utilizes precursor‐level high mass accuracy…”
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Discovering Known and Unanticipated Protein Modifications Using MS/MS Database Searching by Tang, Wilfred H, Halpern, Benjamin R, Shilov, Ignat V, Seymour, Sean L, Keating, Sean P, Loboda, Alex, Patel, Alpesh A, Schaeffer, Daniel A, Nuwaysir, Lydia M

“…We present an MS/MS database search algorithm with the following novel features:  (1) a novel protein database structure containing extensive preindexing and…”
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Comparison of Rates and Kinetic Isotope Effects Using PEG-Modified Variants and Glycoforms of Glucose Oxidase:  The Relationship of Modification of the Protein Envelope to C−H Activation and Tunneling by Seymour, Sean L, Klinman, Judith P

“…An earlier investigation of the temperature dependencies of rates and kinetic isotope effects (KIEs) in glucose oxidase (GO) used variants that differed in the…”
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Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles) by Kinsinger, Christopher R., Apffel, James, Baker, Mark, Bian, Xiaopeng, Borchers, Christoph H., Bradshaw, Ralph, Brusniak, Mi-Youn, Chan, Daniel W., Deutsch, Eric W., Domon, Bruno, Gorman, Jeff, Grimm, Rudolf, Hancock, William, Hermjakob, Henning, Horn, David, Hunter, Christie, Kolar, Patrik, Kraus, Hans-Joachim, Langen, Hanno, Linding, Rune, Moritz, Robert L., Omenn, Gilbert S., Orlando, Ron, Pandey, Akhilesh, Ping, Peipei, Rahbar, Amir, Rivers, Robert, Seymour, Sean L., Simpson, Richard J., Slotta, Douglas, Smith, Richard D., Stein, Stephen E., Tabb, David L., Tagle, Danilo, Yates III, John R., Rodriguez, Henry

“…Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking…”
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