Ghent University Academic Bibliography

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- Miscellaneous
- open access
A comprehensive evaluation of consensus spectrum generation methods in proteomics

Xiyang Luo, Wout Bittremieux, Johannes Griss, Eric W Deutsch, Timo Sachsenberg, Lev I Levitsky, Mark V Ivanov, Julia A Bubis, Ralf Gabriels (UGent) , Henry Webel, et al.

(2022) bioRxiv.
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- Conference Paper
- C3
- open access
The HUPO-PSI standardized spectral library format

Ralf Gabriels (UGent) , Nuno Bandeira, Wout Bittremieux, Jeremy J Carver, Matthew Chambers, Shin Kawano, Henry Lam, Tytus Mak, Yasset Perez-Riverol, Benjamin J Pullman, et al.

(2020) EuBIC 2020 developers' meeting.
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Proteomics Standards Initiative extended FASTA format

Pierre-Alain Binz, Jim Shofstahl, Juan Antonio Vizcaíno, Harald Barsnes, Robert J Chalkley, Gerben Menschaert (UGent) , Emanuele Alpi, Karl Clauser, Jimmy K Eng, Lydie Lane, et al.

(2019) JOURNAL OF PROTEOME RESEARCH. 18(6). p.2686-2692
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- Journal Article
- A1
- open access
The proBAM and proBed standard formats : enabling a seamless integration of genomics and proteomics data

Gerben Menschaert (UGent) , Xiaojing Wang, Andrew R Jones, Fawaz Ghali, David Fenyö, Volodimir Olexiouk (UGent) , Bing Zhang, Eric W Deutsch, Tobias Ternent and Juan Antonio Vizcaíno

(2018) GENOME BIOLOGY. 19.
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Expanding the use of spectral libraries in proteomics

Eric W Deutsch, Yasset Perez-Riverol, Robert J Chalkley, Mathias Wilhelm, Stephen Tate, Timo Sachsenberg, Mathias Walzer, Lukas Käll, Bernard Delanghe, Sebastian Böcker, et al.

(2018) JOURNAL OF PROTEOME RESEARCH. 17(12). p.4051-4060
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- Miscellaneous
Proteomics Standards Initiative : fifteen years of progress and future work

Eric W Deutsch, Sandra Orchard, Pierre-Alain Binz, Wout Bittremieux, Martin Eisenacher, Henning Hermjakob, Shin Kawano, Henry Lam, Gerhard Mayer, Gerben Menschaert (UGent) , et al.

(2017) JOURNAL OF PROTEOME RESEARCH. 16(12). p.4288-4298
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- Miscellaneous
Human proteome project mass spectrometry data interpretation guidelines 2.1

Eric W Deutsch, Christopher M Overall, Jennifer E Van Eyk, Mark S Baker, Young-Ki Paik, Susan T Weintraub, Lydie Lane, Lennart Martens (UGent) , Yves Vandenbrouck, Ulrike Kusebauch, et al.

(2016) JOURNAL OF PROTEOME RESEARCH. 15(11). p.3961-3970
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ProteomeXchange provides globally coordinated proteomics data submission and dissemination

Juan A Vizcaino, Eric W Deutsch, Rui Wang, Attila Csordas, Florian Reisinger, Daniel Ríos, José A Dianes, Zhi Sun, Terry Farrah, Nuno Bandeira, et al.

(2014) NATURE BIOTECHNOLOGY. 32(3). p.223-226
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TraML: a standard format for exchange of selected reaction monitoring transition lists

Eric W Deutsch, Matthew Chambers, Steffen Neumann, Fredrik Levander, Pierre-Alain Binz, Jim Shofstahl, David S Campbell, Luis Mendoza, David Ovelleiro, Kenny Helsens (UGent) , et al.

(2012) MOLECULAR & CELLULAR PROTEOMICS. 11(4).
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The HUPO initiative on Model Organism Proteomes, iMOP

Alexandre ME Jones, Ruedi Aebersold, Christian H Ahrens, Rolf Apweiler, Katja Baerenfaller, Mark Baker, Emøke Bendixen, Steve Briggs, Philip Brownridge, Erich Brunner, et al.

(2012) PROTEOMICS. 12(3). p.340-345

Academic Bibliography

A comprehensive evaluation of consensus spectrum generation methods in proteomics

The HUPO-PSI standardized spectral library format

Proteomics Standards Initiative extended FASTA format

The proBAM and proBed standard formats : enabling a seamless integration of genomics and proteomics data

Expanding the use of spectral libraries in proteomics

Proteomics Standards Initiative : fifteen years of progress and future work

Human proteome project mass spectrometry data interpretation guidelines 2.1

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

TraML: a standard format for exchange of selected reaction monitoring transition lists

The HUPO initiative on Model Organism Proteomes, iMOP

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