File Formats Commonly Used in Mass Spectrometry Proteomics*

by Deutsch, Eric W.
Published 2012

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

by Malmström, Johan, Beck, Martin, Schmidt, Alexander, Lange, Vinzenz, Deutsch, Eric W., Aebersold, Ruedi
Published 2009

SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology

by Marzolf, Bruz, Deutsch, Eric W, Moss, Patrick, Campbell, David, Johnson, Michael H, Galitski, Timothy
Published 2006

The urologic epithelial stem cell database (UESC) – a web tool for cell type-specific gene expression and immunohistochemistry images of the prostate and bladder

by Pascal, Laura E, Deutsch, Eric W, Campbell, David S, Korb, Martin, True, Lawrence D, Liu, Alvin Y
Published 2007

A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues

by Chan, Queenie WT, Parker, Robert, Sun, Zhi, Deutsch, Eric W, Foster, Leonard J
Published 2011

Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1

by Bonneau, Richard, Baliga, Nitin S, Deutsch, Eric W, Shannon, Paul, Hood, Leroy
Published 2004

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework

by Lewis, Steven, Csordas, Attila, Killcoyne, Sarah, Hermjakob, Henning, Hoopmann, Michael R, Moritz, Robert L, Deutsch, Eric W, Boyle, John
Published 2012

The PeptideAtlas project

by Desiere, Frank, Deutsch, Eric W., King, Nichole L., Nesvizhskii, Alexey I., Mallick, Parag, Eng, Jimmy, Chen, Sharon, Eddes, James, Loevenich, Sandra N., Aebersold, Ruedi
Published 2006

Development of data representation standards by the human proteome organization proteomics standards initiative

by Deutsch, Eric W, Albar, Juan Pablo, Binz, Pierre-Alain, Eisenacher, Martin, Jones, Andrew R, Mayer, Gerhard, Omenn, Gilbert S, Orchard, Sandra, Vizcaíno, Juan Antonio, Hermjakob, Henning
Published 2015

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

by King, Nichole L, Deutsch, Eric W, Ranish, Jeffrey A, Nesvizhskii, Alexey I, Eddes, James S, Mallick, Parag, Eng, Jimmy, Desiere, Frank, Flory, Mark, Martin, Daniel B, Kim, Bong, Lee, Hookeun, Raught, Brian, Aebersold, Ruedi
Published 2006

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

by Brusniak, Mi-Youn K, Kwok, Sung-Tat, Christiansen, Mark, Campbell, David, Reiter, Lukas, Picotti, Paola, Kusebauch, Ulrike, Ramos, Hector, Deutsch, Eric W, Chen, Jingchun, Moritz, Robert L, Aebersold, Ruedi
Published 2011

TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists*

by Deutsch, Eric W., Chambers, Matthew, Neumann, Steffen, Levander, Fredrik, Binz, Pierre-Alain, Shofstahl, Jim, Campbell, David S., Mendoza, Luis, Ovelleiro, David, Helsens, Kenny, Martens, Lennart, Aebersold, Ruedi, Moritz, Robert L., Brusniak, Mi-Youn
Published 2012

The mzQuantML Data Standard for Mass Spectrometry–based Quantitative Studies in Proteomics*

by Walzer, Mathias, Qi, Da, Mayer, Gerhard, Uszkoreit, Julian, Eisenacher, Martin, Sachsenberg, Timo, Gonzalez-Galarza, Faviel F., Fan, Jun, Bessant, Conrad, Deutsch, Eric W., Reisinger, Florian, Vizcaíno, Juan Antonio, Medina-Aunon, J. Alberto, Albar, Juan Pablo, Kohlbacher, Oliver, Jones, Andrew R.
Published 2013

Controlled vocabularies and ontologies in proteomics: Overview, principles and practice☆

by Mayer, Gerhard, Jones, Andrew R., Binz, Pierre-Alain, Deutsch, Eric W., Orchard, Sandra, Montecchi-Palazzi, Luisa, Vizcaíno, Juan Antonio, Hermjakob, Henning, Oveillero, David, Julian, Randall, Stephan, Christian, Meyer, Helmut E., Eisenacher, Martin
Published 2014

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

by Mayer, Gerhard, Montecchi-Palazzi, Luisa, Ovelleiro, David, Jones, Andrew R., Binz, Pierre-Alain, Deutsch, Eric W., Chambers, Matthew, Kallhardt, Marius, Levander, Fredrik, Shofstahl, James, Orchard, Sandra, Antonio Vizcaíno, Juan, Hermjakob, Henning, Stephan, Christian, Meyer, Helmut E., Eisenacher, Martin
Published 2013

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
Published 2012

ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination

by Vizcaíno, Juan A., Deutsch, Eric W., Wang, Rui, Csordas, Attila, Reisinger, Florian, Ríos, Daniel, Dianes, José A., Sun, Zhi, Farrah, Terry, Bandeira, Nuno, Binz, Pierre-Alain, Xenarios, Ioannis, Eisenacher, Martin, Mayer, Gerhard, Gatto, Laurent, Campos, Alex, Chalkley, Robert J., Kraus, Hans-Joachim, Albar, Juan Pablo, Martinez-Bartolomé, Salvador, Apweiler, Rolf, Omenn, Gilbert S., Martens, Lennart, Jones, Andrew R., Hermjakob, Henning
Published 2014

Predictive Big Data Analytics: A Study of Parkinson’s Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations

by Dinov, Ivo D., Heavner, Ben, Tang, Ming, Glusman, Gustavo, Chard, Kyle, Darcy, Mike, Madduri, Ravi, Pa, Judy, Spino, Cathie, Kesselman, Carl, Foster, Ian, Deutsch, Eric W., Price, Nathan D., Van Horn, John D., Ames, Joseph, Clark, Kristi, Hood, Leroy, Hampstead, Benjamin M., Dauer, William, Toga, Arthur W.
Published 2016

An open-source computational and data resource to analyze digital maps of immunopeptidomes

by Caron, Etienne, Espona, Lucia, Kowalewski, Daniel J, Schuster, Heiko, Ternette, Nicola, Alpízar, Adán, Schittenhelm, Ralf B, Ramarathinam, Sri H, Lindestam Arlehamn, Cecilia S, Chiek Koh, Ching, Gillet, Ludovic C, Rabsteyn, Armin, Navarro, Pedro, Kim, Sangtae, Lam, Henry, Sturm, Theo, Marcilla, Miguel, Sette, Alessandro, Campbell, David S, Deutsch, Eric W, Moritz, Robert L, Purcell, Anthony W, Rammensee, Hans-Georg, Stevanovic, Stefan, Aebersold, Ruedi
Published 2015

A repository of assays to quantify 10,000 human proteins by SWATH-MS

by Rosenberger, George, Koh, Ching Chiek, Guo, Tiannan, Röst, Hannes L., Kouvonen, Petri, Collins, Ben C., Heusel, Moritz, Liu, Yansheng, Caron, Etienne, Vichalkovski, Anton, Faini, Marco, Schubert, Olga T., Faridi, Pouya, Ebhardt, H. Alexander, Matondo, Mariette, Lam, Henry, Bader, Samuel L., Campbell, David S., Deutsch, Eric W., Moritz, Robert L., Tate, Stephen, Aebersold, Ruedi
Published 2014