Výsledky vyhledávání - "Frederic Nikitin"

The neXtProt knowledgebase in 2020: data, tools and usability improvements

Autor: Kasun Samarasinghe, Amos Marc Bairoch, Valentine Rech de Laval, Lydie Lane, Monique Zahn-Zabal, Pierre-André Michel, Daniel Dinis Teixeira, Pascale Gaudet, Mathieu Schaeffer, Estelle Audot, Paula D. Duek, Frederic Nikitin, Alain Gateau

Publikováno v: Nucleic Acids Research
Nucleic Acids Research, Vol. 48 (2020) pp. D328-D334

The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describ

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e6be370e8ae094c653b21997ce619519
http://europepmc.org/articles/PMC7145669

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Optimization by infusion of multiple reaction monitoring transitions for sensitive quantification of peptides by liquid chromatography/mass spectrometry

Autor: Gérard Hopfgartner, Thomas Stricker, Markus Müller, Caterina Strambio-De-Castillia, Jeremy Luban, Eva Duchoslav, Emmanuel Varesio, Bandar Alghanem, Frédérique Lisacek, Frederic Nikitin

Publikováno v: Rapid Communications in Mass Spectrometry. 31:753-761

Rationale In peptide quantification by liquid chromatography/mass spectrometry (LC/MS), the optimization of multiple reaction monitoring (MRM) parameters is essential for sensitive detection. We have compared different approaches to build MRM assays,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::f57d79733a503ba2b9629a8c34c5290f
https://doi.org/10.1002/rcm.7839

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The neXtProt knowledgebase on human proteins: 2017 update

Autor: Pierre-André Michel, Marcin J. Domagalski, Frederic Nikitin, Pascale Gaudet, Lydie Lane, Aurore Britan, Valérie Hinard, Mathieu Schaeffer, Anne Gleizes, Valentine Rech de Laval, JinJin Lin, Daniel Dinis Teixeira, Amos Marc Bairoch, Paula D. Duek, Monique Zahn-Zabal, Isabelle Cusin, Alain Gateau

Publikováno v: Nucleic Acids Research, Vol. 45, No D1 (2017) pp. D177-D182
Nucleic Acids Research

The neXtProt human protein knowledgebase (https://www.nextprot.org) continues to add new content and tools, with a focus on proteomics and genetic variation data. neXtProt now has proteomics data for over 85% of the human proteins, as well as new too

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2ac98b4a78d867257d72ba37f3fa6c44
https://doi.org/10.1093/nar/gkw1062

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An improved method for the construction of decoy peptide MS/MS spectra suitable for the accurate estimation of false discovery rates

Autor: Erik Ahrné, Alexander Scherl, Markus Müller, Frédérique Lisacek, Yuki Ohta, Frederic Nikitin

Publikováno v: Proteomics

The relevance of libraries of annotated MS/MS spectra is growing with the amount of proteomic data generated in high-throughput experiments. These reference libraries provide a fast and accurate way to identify newly acquired MS/MS spectra. In the co

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::241e1f42e40a7a9d8245fd9cc5c792fa
https://doi.org/10.1002/pmic.201000665

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QuickMod: A tool for open modification spectrum library searches

Autor: Markus Müller, Frederic Nikitin, Erik Ahrné, Frédérique Lisacek

Publikováno v: Journal of proteome research

MS2 library spectra are rich in reproducible information about peptide fragmentation patterns compared to theoretical spectra modeled by a sequence search tool. So far, spectrum library searches are mostly applied to detect peptides as they are prese

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4c5ccb0c319a6b3dd2e2efd43dfd33e5

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MzJava: An open source library for mass spectrometry data processing

Autor: Oliver Horlacher, Davide Alocci, Markus Müller, Frédérique Lisacek, Julien Mariethoz, Frederic Nikitin

Publikováno v: Journal of proteomics, Vol. 129 (2015) pp. 63-70
Journal of Proteomics

Mass spectrometry (MS) is a widely used and evolving technique for the high-throughput identification of molecules in biological samples. The need for sharing and reuse of code among bioinformaticians working with MS data prompted the design and impl

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e8f355a299d81744dc4d3e4625f050c8
https://archive-ouverte.unige.ch/unige:159524

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Shaping Biological Knowledge: Applications in Proteomics

Autor: Pedro Gonnet, S. Kappus, Frederic Nikitin, Grégoire Rossier, Christine Chichester, P. Roland, Frédérique Lisacek, Ron D. Appel, L. Truong, O. Jaillet

Publikováno v: Comparative and Functional Genomics
Comparative and Functional Genomics, Vol 5, Iss 2, Pp 190-195 (2004)
Comparative and Functional Genomics, Vol 5, Iss 2, Pp 190-195 (2006)

The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splic

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3dfdc955b4ace9f0b6c191b55c9114a6
https://doi.org/10.1002/cfg.379

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Investigating protein domain combinations in complete proteomes

Autor: Frédérique Lisacek, Frederic Nikitin

Publikováno v: Computational Biology and Chemistry. 27:481-495

Protein-related information is more accumulated rather than reduced to a synthetic view. Itemising properties of protein sequences is informative, so is the list of ingredients to do some cooking, but without a recipe, that is, quantification and chr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2132a2e662135e84be1bffe122776044
https://doi.org/10.1016/j.compbiolchem.2003.09.003

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Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding

Autor: Frederic Nikitin, Miki Hasegawa, Frédérique Lisacek, Oliver Horlacher, Hidehiko Fujinaka, Ying Zhang, Naohiko Kinoshita, Bo Xu, Samuel Garessus, Tadashi Yamamoto, Yutaka Yoshida, Eishin Yaoita, Markus Müller, Sameh Magdeldin

Publikováno v: Proteomics. 15(15)

Formalin-fixed paraffin-embedded (FFPE) tissue is considered as an appropriate alternative to frozen/fresh tissue for proteomic analysis. Here we study formalin-induced alternations on a proteome-wide level. We compared LC-MS/MS data of FFPE and froz

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1afb5f393f75ca14a9a5b24955ae0a14
https://pubmed.ncbi.nlm.nih.gov/25825003

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Clustering and filtering tandem mass spectra acquired in data-independent mode

Autor: Florent Gluck, Alexander Scherl, Hui Song Pak, Frédérique Lisacek, Markus Müller, Frederic Nikitin

Publikováno v: Journal of the American Society for Mass Spectrometry, Vol. 24, No 12 (2013) pp. 1862-1871
J Am Soc Mass Spectrom

Data-independent mass spectrometry activates all ion species isolated within a given mass-to-charge window (m/z) regardless of their abundance. This acquisition strategy overcomes the traditional data-dependent ion selection boosting data reproducibi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::07557f448272cc262bd593808461e3e7
https://pubmed.ncbi.nlm.nih.gov/24006250

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