Eric W Deutsch

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 83

Top Venues

Journal of proteome research

bioRxiv : the preprint server for biology

GeroScience

Nature biotechnology

Institute for Systems Biology

University of Washington (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Institute for Systems Biology

United States

Senior Research Scientist

Microsoft Corp

United States

Senior Systems Engineer

University of Washington

United States

Post-Doctoral Researcher :: Astronomy

Education History

University of Washington

United States

PHD

Publications

Kerry A Ramsbottom, Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Zhi Sun, Deepti J Kundu, Emily Bowler-Barnett, Maria Martin, Jun Fan, Dmytro Chebotarov, Kenneth L McNally, Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones
Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome. Journal of proteome research (2024)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Cecilia Lindskog, Charles Pineau, Nicolle H Packer, Ileana M Cristea, Susan T Weintraub, Sandra E Orchard, Michael H A Roehrl, Edouard Collins Nice, Tiannan Guo, Jennifer E Van Eyk, Siqi Liu, Nuno Bandeira, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch
The 2023 Report on the Proteome from the HUPO Human Proteome Project. Journal of proteome research 23 (2) (2024)
Klaas J van Wijk, Tami Leppert, Zhi Sun, Isabell Guzchenko, Erica Debley, Georgia Sauermann, Pratyush Routray, Luis Mendoza, Qi Sun, Eric W Deutsch
The Zea mays PeptideAtlas: A New Maize Community Resource. Journal of proteome research (2024)
Kerry A Ramsbottom, Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Zhi Sun, Deepti J Kundu, Emily Bowler-Barnett, Maria Martin, Jun Fan, Dmytro Chebotarov, Kenneth L McNally, Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones
Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome. Journal of proteome research 23 (7) (2024)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Cecilia Lindskog, Charles Pineau, Nicolle H Packer, Ileana M Cristea, Susan T Weintraub, Sandra E Orchard, Michael H A Roehrl, Edouard Collins Nice, Tiannan Guo, Jennifer E Van Eyk, Siqi Liu, Nuno Bandeira, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch
The 2023 Report on the Proteome from the HUPO Human Proteome Project. Journal of proteome research 23 (2) (2024)
Kerry A Ramsbottom, Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Zhi Sun, Deepti J Kundu, Emily Bowler-Barnett, Maria Martin, Jun Fan, Dmytro Chebotarov, Kenneth L McNally, Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones
Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome. Journal of proteome research 23 (7) (2024)
Kerry A Ramsbottom, Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Zhi Sun, Deepti J Kundu, Emily Bowler-Barnett, Maria Martin, Jun Fan, Dmytro Chebotarov, Kenneth L McNally, Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones
Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome. Journal of proteome research (2024)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Cecilia Lindskog, Charles Pineau, Nicolle H Packer, Ileana M Cristea, Susan T Weintraub, Sandra E Orchard, Michael H A Roehrl, Edouard Collins Nice, Tiannan Guo, Jennifer E Van Eyk, Siqi Liu, Nuno Bandeira, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch
The 2023 Report on the Proteome from the HUPO Human Proteome Project. Journal of proteome research 23 (2) (2024)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Cecilia Lindskog, Charles Pineau, Nicolle H Packer, Ileana M Cristea, Susan T Weintraub, Sandra E Orchard, Michael H A Roehrl, Edouard Collins Nice, Tiannan Guo, Jennifer E Van Eyk, Siqi Liu, Nuno Bandeira, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch
The 2023 Report on the Proteome from the HUPO Human Proteome Project. Journal of proteome research 23 (2) (2024)
Nathan H Zhang, Eric W Deutsch
SpectiCal: m / z Calibration of MS2 Peptide Spectra Using Known Low Mass Ions. Journal of proteome research 23 (4) (2024)
Nathan H Zhang, Eric W Deutsch
SpectiCal: m / z Calibration of MS2 Peptide Spectra Using Known Low Mass Ions. Journal of proteome research 23 (4) (2024)
Nathan H Zhang, Eric W Deutsch
SpectiCal: m / z Calibration of MS2 Peptide Spectra Using Known Low Mass Ions. Journal of proteome research 23 (4) (2024)
Kerry A Ramsbottom, Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Zhi Sun, Deepti J Kundu, Emily Bowler-Barnett, Maria Martin, Jun Fan, Dmytro Chebotarov, Kenneth L McNally, Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones
Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome. Journal of proteome research 23 (7) (2024)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Cecilia Lindskog, Charles Pineau, Nicolle H Packer, Ileana M Cristea, Susan T Weintraub, Sandra E Orchard, Michael H A Roehrl, Edouard Collins Nice, Tiannan Guo, Jennifer E Van Eyk, Siqi Liu, Nuno Bandeira, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch
The 2023 Report on the Proteome from the HUPO Human Proteome Project. Journal of proteome research 23 (2) (2024)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Cecilia Lindskog, Charles Pineau, Nicolle H Packer, Ileana M Cristea, Susan T Weintraub, Sandra E Orchard, Michael H A Roehrl, Edouard Collins Nice, Tiannan Guo, Jennifer E Van Eyk, Siqi Liu, Nuno Bandeira, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch
The 2023 Report on the Proteome from the HUPO Human Proteome Project. Journal of proteome research 23 (2) (2024)
Klaas J van Wijk, Tami Leppert, Zhi Sun, Isabell Guzchenko, Erica Debley, Georgia Sauermann, Pratyush Routray, Luis Mendoza, Qi Sun, Eric W Deutsch
The Zea mays PeptideAtlas: A New Maize Community Resource. Journal of proteome research (2024)
Kerry A Ramsbottom, Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Zhi Sun, Deepti J Kundu, Emily Bowler-Barnett, Maria Martin, Jun Fan, Dmytro Chebotarov, Kenneth L McNally, Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones
Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome. Journal of proteome research 23 (7) (2024)
Nathan H Zhang, Eric W Deutsch
SpectiCal: m / z Calibration of MS2 Peptide Spectra Using Known Low Mass Ions. Journal of proteome research (2024)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Cecilia Lindskog, Charles Pineau, Nicolle H Packer, Ileana M Cristea, Susan T Weintraub, Sandra E Orchard, Michael H A Roehrl, Edouard Collins Nice, Tiannan Guo, Jennifer E Van Eyk, Siqi Liu, Nuno Bandeira, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch
The 2023 Report on the Proteome from the HUPO Human Proteome Project. Journal of proteome research (2024)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy J Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Klaas J van Wijk, Tami Leppert, Zhi Sun, Alyssa Kearly, Margaret Li, Luis Mendoza, Isabell Guzchenko, Erica Debley, Georgia Sauermann, Pratyush Routray, Sagunya Malhotra, Andrew Nelson, Qi Sun, Eric W Deutsch
Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas. Journal of proteome research 23 (1) (2023)
Eric W Deutsch, Luis Mendoza, David D Shteynberg, Michael R Hoopmann, Zhi Sun, Jimmy K Eng, Robert L Moritz
Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite. Journal of proteome research 22 (2) (2023)
Klaas J van Wijk, Tami Leppert, Zhi Sun, Alyssa Kearly, Margaret Li, Luis Mendoza, Isabell Guzchenko, Erica Debley, Georgia Sauermann, Pratyush Routray, Sagunya Malhotra, Andrew Nelson, Qi Sun, Eric W Deutsch
Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas. Journal of proteome research (2023)
John R Prensner, Jennifer G Abelin, Leron W Kok, Karl R Clauser, Jonathan M Mudge, Jorge Ruiz-Orera, Michal Bassani-Sternberg, Eric W Deutsch, Sebastiaan van Heesch
What can Ribo-seq and proteomics tell us about the non-canonical proteome? bioRxiv : the preprint server for biology (2023)
Tobias Greisager Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A Neely, Magnus Palmblad, Yasset Perez Riverol, Tobias K Schmidt, Juan Antonio Vizcaino, Eric W Deutsch
ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics. Journal of proteome research 22 (2) (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy J Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research (2023)
Adam R Burns, Jack Wiedrick, Alicia Feryn, David H Baxter, Mukul K Midha, Seamus R Morrone, Seamus R Morrone, Timothy J Prokop, Michal Maes, Michael R Hoopmann, Ulrike Kusebauch, Eric W Deutsch, Noa Rappaport, Kengo Watanabe, Robert L Moritz, Richard A Miller, Jodi A Lapidus, Eric S Orwoll
Proteomic changes induced by longevity-promoting interventions in mice. GeroScience (2023)
Eric W Deutsch, Luis Mendoza, David D Shteynberg, Michael R Hoopmann, Zhi Sun, Jimmy K Eng, Robert L Moritz
Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite. Journal of proteome research 22 (2) (2023)
Eric W Deutsch, Luis Mendoza, David D Shteynberg, Michael R Hoopmann, Zhi Sun, Jimmy K Eng, Robert L Moritz
Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite. Journal of proteome research (2023)
Tobias Greisager Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A Neely, Magnus Palmblad, Yasset Perez Riverol, Tobias K Schmidt, Juan Antonio Vizcaino, Eric W Deutsch
ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics. Journal of proteome research 22 (2) (2023)
Klaas J van Wijk, Tami Leppert, Zhi Sun, Eric W Deutsch
Does the Ubiquitination Degradation Pathway Really Reach inside of the Chloroplast? A Re-Evaluation of Mass Spectrometry-Based Assignments of Ubiquitination. Journal of proteome research (2023)
Klaas J van Wijk, Tami Leppert, Zhi Sun, Eric W Deutsch
Does the Ubiquitination Degradation Pathway Really Reach inside of the Chloroplast? A Re-Evaluation of Mass Spectrometry-Based Assignments of Ubiquitination. Journal of proteome research (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy J Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Tobias Greisager Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A Neely, Magnus Palmblad, Yasset Perez Riverol, Tobias K Schmidt, Juan Antonio Vizcaino, Eric W Deutsch
ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics. Journal of proteome research (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy J Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research (2023)
Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H Payne, Tobias Greisager Rehfeldt, Tobias K Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of proteome research (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy J Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H Payne, Tobias Greisager Rehfeldt, Tobias K Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of proteome research 22 (3) (2023)
Tobias Greisager Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A Neely, Magnus Palmblad, Yasset Perez Riverol, Tobias K Schmidt, Juan Antonio Vizcaino, Eric W Deutsch
ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics. Journal of proteome research 22 (2) (2023)
Klaas J van Wijk, Tami Leppert, Zhi Sun, Eric W Deutsch
Does the Ubiquitination Degradation Pathway Really Reach inside of the Chloroplast? A Re-Evaluation of Mass Spectrometry-Based Assignments of Ubiquitination. Journal of proteome research (2023)
Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H Payne, Tobias Greisager Rehfeldt, Tobias K Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of proteome research 22 (3) (2023)
Klaas J van Wijk, Tami Leppert, Zhi Sun, Alyssa Kearly, Margaret Li, Luis Mendoza, Isabell Guzchenko, Erica Debley, Georgia Sauermann, Pratyush Routray, Sagunya Malhotra, Andrew Nelson, Qi Sun, Eric W Deutsch
Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas. Journal of proteome research 23 (1) (2023)
Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H Payne, Tobias Greisager Rehfeldt, Tobias K Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of proteome research 22 (3) (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy J Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Klaas J van Wijk, Tami Leppert, Zhi Sun, Alyssa Kearly, Margaret Li, Luis Mendoza, Isabell Guzchenko, Erica Debley, Georgia Sauermann, Pratyush Routray, Sagunya Malhotra, Andrew Nelson, Qi Sun, Eric W Deutsch
Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas. Journal of proteome research 23 (1) (2023)
Tobias Greisager Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A Neely, Magnus Palmblad, Yasset Perez Riverol, Tobias K Schmidt, Juan Antonio Vizcaino, Eric W Deutsch
ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics. Journal of proteome research (2023)
Klaas J van Wijk, Tami Leppert, Zhi Sun, Alyssa Kearly, Margaret Li, Luis Mendoza, Isabell Guzchenko, Erica Debley, Georgia Sauermann, Pratyush Routray, Sagunya Malhotra, Andrew Nelson, Qi Sun, Eric W Deutsch
Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas. Journal of proteome research (2023)
Tobias Greisager Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A Neely, Magnus Palmblad, Yasset Perez Riverol, Tobias K Schmidt, Juan Antonio Vizcaino, Eric W Deutsch
ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics. Journal of proteome research 22 (2) (2023)
Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H Payne, Tobias Greisager Rehfeldt, Tobias K Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of proteome research 22 (3) (2023)
Tobias Greisager Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A Neely, Magnus Palmblad, Yasset Perez Riverol, Tobias K Schmidt, Juan Antonio Vizcaino, Eric W Deutsch
ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics. Journal of proteome research 22 (2) (2023)
Eric W Deutsch, Luis Mendoza, David D Shteynberg, Michael R Hoopmann, Zhi Sun, Jimmy K Eng, Robert L Moritz
Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite. Journal of proteome research 22 (2) (2023)
Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H Payne, Tobias Greisager Rehfeldt, Tobias K Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of proteome research 22 (3) (2023)
Klaas J van Wijk, Stéphane Bentolila, Tami Leppert, Qi Sun, Zhi Sun, Luis Mendoza, Margaret Li, Eric W Deutsch
Detection and editing of the updated Arabidopsis plastid- and mitochondrial-encoded proteomes through PeptideAtlas. Plant physiology (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy J Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Klaas J van Wijk, Tami Leppert, Zhi Sun, Alyssa Kearly, Margaret Li, Luis Mendoza, Isabell Guzchenko, Erica Debley, Georgia Sauermann, Pratyush Routray, Sagunya Malhotra, Andrew D L Nelson, Qi Sun, Eric W Deutsch
Mapping the Arabidopsis thaliana proteome in PeptideAtlas and the nature of the unobserved (dark) proteome; strategies towards a complete proteome. bioRxiv : the preprint server for biology (2023)
Kerry A Ramsbottom, Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Maria-Jesus Martin, Juan Antonio Vizcaino, Eric W Deutsch, Andrew R Jones
Method for Independent Estimation of the False Localization Rate for Phosphoproteomics. Journal of proteome research 21 (7) (2022)
Klaas J van Wijk, Tami Leppert, Qi Sun, Sascha S Boguraev, Zhi Sun, Luis Mendoza, Eric W Deutsch
The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource. The Plant cell 33 (11) (2022)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Charles Pineau, Nicolle H Packer, Ileana M Cristea, Cecilia Lindskog, Susan T Weintraub, Sandra E Orchard, Michael H A Roehrl, Edouard Collins Nice, Siqi Liu, Nuno Bandeira, Yi-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch
The 2022 Report on the Human Proteome from the HUPO Human Proteome Project. Journal of proteome research (2022)
Xiyang Luo, Wout Bittremieux, Johannes Griss, Eric W Deutsch, Timo Sachsenberg, Lev I Levitsky, Mikhail V Gorshkov, Julia A Bubis, Ralf Gabriels, Henry Webel, Aniel Sanchez, Mingze Bai, Lukas Käll, Yasset Perez Riverol
A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics. Journal of proteome research 21 (6) (2022)
Jonathan M Mudge, Jorge Ruiz-Orera, John R Prensner, Marie A Brunet, Ferriol Calvet, Irwin Jungreis, Jose Manuel Gonzalez, Michele Magrane, Cholsoon Jang, Jana Felicitas Schulz, Yucheng T Yang, M Mar Albà, Julie L Aspden, Pavel V Baranov, Ariel Alejandro Bazzini, Elspeth A Bruford, Maria Jesus Martin, Lorenzo Calviello, Anne-Ruxandra Carvunis, Jin Chen, Juan Pablo Couso, Eric W Deutsch, Paul Flicek, Adam Frankish, Mark Gerstein, Norbert Hübner, Nicholas T Ingolia, Manolis Kellis, Gerben Menschaert, Robert L Moritz, Uwe Ohler, Xavier Roucou, Alan Saghatelian, Jonathan S Weissman, Sebastiaan van Heesch
Standardized annotation of translated open reading frames. Nature biotechnology 40 (7) (2022)
Anton Kalyuzhnyy, Patrick A Eyers, Claire E Eyers, Emily Bowler-Barnett, Maria J Martin, Zhi Sun, Eric W Deutsch, Andrew R Jones
Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation. Journal of proteome research 21 (6) (2022)
Richard D LeDuc, Eric W Deutsch, Pierre-Alain Binz, Ryan T Fellers, Anthony J Cesnik, Joshua A Klein, Tim Van Den Bossche, Ralf Gabriels, Arshika Yalavarthi, Yasset Perez Riverol, Jeremy Carver, Wout Bittremieux, Shin Kawano, Benjamin Pullman, Nuno Bandeira, Michael P Snyder, Paul M Thomas, Juan Antonio Vizcaino
Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. Journal of proteome research 21 (4) (2022)
Eric W Deutsch, Yasset Perez Riverol, Jeremy Carver, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Pierre-Alain Binz, Benjamin Pullman, Zhi Sun, Jim Shofstahl, Wout Bittremieux, Tytus D Mak, Joshua Klein, Yunping Zhu, Henry H N Lam, Juan Antonio Vizcaino, Nuno Bandeira
Universal Spectrum Identifier for mass spectra. Nature methods 18 (7) (2021)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Young-Ki Paik, Ileana M Cristea, Fernando José Corrales, Cecilia Lindskog, Susan T Weintraub, Michael H A Roehrl, Siqi Liu, Nuno Bandeira, Sudhir Srivastava, Yi-Ju Chen, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch
Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project. Journal of proteome research 20 (12) (2021)
Tobias K Schmidt, Patroklos Samaras, Viktoria Dorfer, Christian Panse, Tobias Kockmann, Leon Bichmann, Bart van Puyvelde, Yasset Perez Riverol, Eric W Deutsch, Bernhard Kuster, Mathias Wilhelm
Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison. Journal of proteome research 20 (6) (2021)
Eric W Deutsch, Gilbert S Omenn, Zhi Sun, David H Baxter, Maria Pernemalm, Krishnan K Palaniappan, Natasha Letunica, Yves Vandenbrouck, Virginie Brun, Sheng-Ce Tao, Xiaobo Yu, Philipp E Geyer, Vera Ignjatovic, Robert L Moritz, Jochen M Schwenk
Advances and Utility of the Human Plasma Proteome. Journal of proteome research 20 (12) (2021)
Young-Ki Paik, Christopher M Overall, Fernando José Corrales, Eric W Deutsch, Lydie Lane, Gilbert S Omenn
Advances in Identifying and Characterizing the Human Proteome. Journal of proteome research 18 (12) (2020)
Ranjeet S Bhamber, Andris Jankevics, Eric W Deutsch, Andrew R Jones, Andrew W Dowsey
mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements. Journal of proteome research 20 (1) (2020)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Ileana M Cristea, Fernando José Corrales, Cecilia Lindskog, Young-Ki Paik, Jennifer E Van Eyk, Siqi Liu, Stephen R Pennington, Michael P Snyder, Mark S Baker, Nuno Bandeira, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch
Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. Journal of proteome research 19 (12) (2020)
Young-Ki Paik, Christopher M Overall, Fernando Corrales, Eric W Deutsch, Lydie Lane, Gilbert S Omenn
Toward Completion of the Human Proteome Parts List: Progress Uncovering Proteins That Are Missing or Have Unknown Function and Developing Analytical Methods. Journal of proteome research 17 (12) (2019)
Pierre-Alain Binz, Jim Shofstahl, Juan Antonio Vizcaíno, Harald Barsnes, Robert J Chalkley, Gerben Menschaert, Emanuele Alpi, Karl Clauser, Jimmy K Eng, Lydie Lane, Sean L Seymour, Luis Francisco Hernández Sánchez, Gerhard Mayer, Martin Eisenacher, Yasset Perez-Riverol, Eugene A Kapp, Luis Mendoza, Peter R Baker, Andrew Collins, Tim Van Den Bossche, Eric W Deutsch
Proteomics Standards Initiative Extended FASTA Format. Journal of proteome research 18 (6) (2019)
David D Shteynberg, Eric W Deutsch, David S Campbell, Michael R Hoopmann, Ulrike Kusebauch, Dave Lee, Luis Mendoza, Mukul K Midha, Zhi Sun, Anthony D Whetton, Robert L Moritz
PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline. Journal of proteome research 18 (12) (2019)
Vera Ignjatovic, Philipp E Geyer, Krishnan K Palaniappan, Jessica E Chaaban, Gilbert S Omenn, Mark S Baker, Eric W Deutsch, Jochen M Schwenk
Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data. Journal of proteome research 18 (12) (2019)
Eric W Deutsch, Lydie Lane, Christopher M Overall, Nuno Bandeira, Mark S Baker, Charles Pineau, Robert L Moritz, Fernando José Corrales, Sandra E Orchard, Jennifer E Van Eyk, Young-Ki Paik, Susan T Weintraub, Yves Vandenbrouck, Gilbert S Omenn
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. Journal of proteome research 18 (12) (2019)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Fernando J Corrales, Jochen M Schwenk, Young-Ki Paik, Jennifer E Van Eyk, Siqi Liu, Stephen Pennington, Michael P Snyder, Mark S Baker, Eric W Deutsch
Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project. Journal of proteome research 18 (12) (2019)
Eric W Deutsch, Yasset Perez Riverol, Robert J Chalkley, Mathias Wilhelm, Stephen Tate, Timo Sachsenberg, Mathias Walzer, Lukas Käll, Bernard Delanghe, Sebastian Böcker, Emma L Schymanski, Paul Wilmes, Viktoria Dorfer, Bernhard Kuster, Pieter-Jan Volders, Nico Jehmlich, Johannes P C Vissers, Dennis W Wolan, Ana Y Wang, Luis Mendoza, Jim Shofstahl, Andrew W Dowsey, Johannes Griss, Reza M Salek, Steffen Neumann, Pierre-Alain Binz, Henry H N Lam, Juan Antonio Vizcaino, Nuno Bandeira, Hannes L Röst
Expanding the Use of Spectral Libraries in Proteomics. Journal of proteome research 17 (12) (2018)
Luis Mendoza, Eric W Deutsch, Zhi Sun, David S Campbell, David D Shteynberg, Robert L Moritz
Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper. Journal of proteome research 17 (12) (2018)
Young-Ki Paik, Christopher M Overall, Eric W Deutsch, Jennifer E Van Eyk, Gilbert S Omenn
Progress and Future Direction of Chromosome-Centric Human Proteome Project. Journal of proteome research 16 (12) (2018)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Fernando José Corrales, Jochen M Schwenk, Young-Ki Paik, Jennifer E Van Eyk, Siqi Liu, Michael Snyder, Mark S Baker, Eric W Deutsch
Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project. Journal of proteome research 17 (12) (2018)
Kristian E Swearingen, Jimmy K Eng, David Shteynberg, Vladimir Vigdorovich, Timothy A Springer, Luis Mendoza, D Noah Sather, Eric W Deutsch, Stefan H I Kappe, Robert L Moritz
A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry. Journal of proteome research 18 (2) (2018)
Gilbert S Omenn, Lydie Lane, Emma K Lundberg, Christopher M Overall, Eric W Deutsch
Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project. Journal of proteome research 16 (12) (2017)
Eric W Deutsch, Sandra Orchard, Pierre-Alain Binz, Wout Bittremieux, Martin Eisenacher, Henning Hermjakob, Shin Kawano, Henry Lam, Gerhard Mayer, Gerben Menschaert, Yasset Perez-Riverol, Reza M Salek, David L Tabb, Stefan Tenzer, Juan Antonio Vizcaíno, Mathias Walzer, Andrew R Jones
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. Journal of proteome research 16 (12) (2017)
Jochen M Schwenk, Gilbert S Omenn, Zhi Sun, David S Campbell, Mark S Baker, Christopher M Overall, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch
The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays. Journal of proteome research 16 (12) (2017)

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Eric W Deutsch