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The neXtProt peptide uniqueness checker: a tool for the proteomics community

Mathieu Schaeffer, Alain Gateau, Daniel Teixeira, Pierre-André Michel, Monique Zahn-Zabal, Lydie Lane, John Hancock
2017 Bioinformatics  
The peptide uniqueness checker tool is freely available on the web at https://www.nextprot.org/tools/peptide-uniqueness-checker and from the neXtProt API at https://api.nextprot.org/.  ...  The neXtProt peptide uniqueness checker allows scientists to define which peptides can be used to validate the existence of human proteins, i.e. map uniquely versus multiply to human protein sequences  ...  The authors thank Amos Bairoch for his insight on the article; Fre ´de ´ric Nikitin, Anne Gleizes and Valentine Rech de Laval for their help in integrating the uniqueness checker in the neXtProt interface  ... 
doi:10.1093/bioinformatics/btx318 pmid:28520855 pmcid:PMC5860159 fatcat:l3gqnsyllzapxhqj5cddt7nrrq

The neXtProt knowledgebase on human proteins: 2017 update

Pascale Gaudet, Pierre-André Michel, Monique Zahn-Zabal, Aurore Britan, Isabelle Cusin, Marcin Domagalski, Paula D. Duek, Alain Gateau, Anne Gleizes, Valérie Hinard, Valentine Rech de Laval, JinJin Lin (+5 others)
2016 Nucleic Acids Research  
over 85% of the human proteins, as well as new tools tailored to the proteomics community.  ...  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  ...  neXtProt with a solid foundation.  ... 
doi:10.1093/nar/gkw1062 pmid:27899619 pmcid:PMC5210547 fatcat:lqlfkjexi5azrdnye7iylyp4he

Flexible and fast mapping of peptides to a proteome with ProteoMapper

Luis Mendoza, Eric W. Deutsch, Zhi Sun, David S Campbell, David D. Shteynberg, Robert L. Moritz
2018 Journal of Proteome Research  
The ProteoMapper tool enables a comprehensive and rapid mapping of peptides to a reference proteome. The indexer component creates a segmented index for an input proteome from a FASTA or PEFF file.  ...  Bottom-up proteomics relies on the proteolytic or chemical cleavage of proteins into peptides, the identification of those peptides via mass spectrometry, and the mapping of the identified peptides back  ...  Acknowledgements This work was funded in part by the National Institutes of Health, National Institute of General Medical Sciences grants: R01GM087221, R24GM127667, P50GM076547, the National Institute  ... 
doi:10.1021/acs.jproteome.8b00544 pmid:30230343 pmcid:PMC6438762 fatcat:vleknfus3rcrbot6tf5lzvkr5e

Toward Completion of the Human Proteome Parts List: Progress Uncovering Proteins That Are Missing or Have Unknown Function and Developing Analytical Methods

Young-Ki Paik, Christopher M. Overall, Fernando Corrales, Eric W. Deutsch, Lydie Lane, Gilbert S. Omenn
2018 Journal of Proteome Research  
They identified peptides from 13 MPs after filtering with the neXtProt uniqueness checker.  ...  The MPs met the HPP Guidelines v2.1.0, 3 requiring two uniquely mapping and non-nested peptides of at least 9 aa, confirmed with the neXtProt uniqueness checker.  ... 
doi:10.1021/acs.jproteome.8b00885 pmid:30985145 pmcid:PMC6288998 fatcat:qv66ies3e5b5dkiudtqixnzzga

Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project

Gilbert S. Omenn, Lydie Lane, Emma K. Lundberg, Christopher M. Overall, Eric W. Deutsch
2017 Journal of Proteome Research  
The Human Proteome Organization (HUPO) Human Proteome Project (HPP) continues to make progress on its two overall goals: (1) completing the protein parts list, with an annual update of the HUPO draft human  ...  proteome, and (2) making proteomics an integrated complement to genomics and transcriptomics throughout biomedical and life sciences research. neXtProt version 2017-01-23 has 17,008 confident protein  ...  We thank the UniProt groups at SIB, EBI, and PIR for providing high-quality annotations for the human proteins in UniProtKB/ Swiss-Prot. The neXtProt server is hosted by VitalIT in Switzerland.  ... 
doi:10.1021/acs.jproteome.7b00375 pmid:28853897 pmcid:PMC5872831 fatcat:kccrhpwwpzhqzjsssoxtqg42ji

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0 [article]

Eric W Deutsch, Lydie Lane, Chris M Overall, Nuno Bandeira, Mark S Baker, Charles Pineau, Robert L Moritz, Fernando Corrales, Sandra Orchard, Jennifer E Van Eyk, Young-Ki Paik, Susan T Weintraub (+2 others)
2019 bioRxiv   pre-print
We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets.  ...  We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards  ...  Despite some useful tools available for authors to address this guideline (e.g., neXtProt peptide uniqueness checker 32 and PeptideAtlas ProteoMapper 33 ), it remains one of the most difficult to fulfill  ... 
doi:10.1101/733576 fatcat:tge7sztiqbfqfk7zotktdhemjy

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0

Eric W. Deutsch, Lydie Lane, Christopher M Overall, Nuno Bandeira, Mark S. Baker, Charles Pineau, Robert L. Moritz, Fernando Corrales, Sandra Orchard, Jennifer E. Van Eyk, Young-Ki Paik, Susan T. Weintraub (+2 others)
2019 Journal of Proteome Research  
Here, we describe an update to these guidelines based on consensus-reaching discussions with the wider HPP community over the past year.  ...  We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by  ...  Despite some useful tools available for authors to address this guideline (e.g., neXtProt peptide uniqueness checker 33 and PeptideAtlas ProteoMapper 34 ), it remains one of the most difficult to fulfill  ... 
doi:10.1021/acs.jproteome.9b00542 pmid:31599596 pmcid:PMC6986310 fatcat:qiplkvgpgfdldco2tw5d34dpea

Accelerating the search for the missing proteins in the human proteome

Mark S. Baker, Seong Beom Ahn, Abidali Mohamedali, Mohammad T. Islam, David Cantor, Peter D. Verhaert, Susan Fanayan, Samridhi Sharma, Edouard C. Nice, Mark Connor, Shoba Ranganathan
2017 Nature Communications  
The Human Proteome Project (HPP) aims to discover high-stringency data for all proteins encoded by the human genome.  ...  Our re-analysis of publicly available MS data for the largest family of missing proteins (olfactory receptors), viewed in conjunction with other specific missing protein examples reveals a need for the  ...  We thank Professor G Omenn, Dr L Lane, Dr E Deutsch, Dr H Cheruku, Ms I Nawar and the HUPO community for helpful discussions during the course of this work.  ... 
doi:10.1038/ncomms14271 pmid:28117396 pmcid:PMC5286205 fatcat:htunxdfvlvgnbbdnc7zizwuddi

A high-stringency blueprint of the human proteome

Subash Adhikari, Edouard C. Nice, Eric W. Deutsch, Lydie Lane, Gilbert S. Omenn, Stephen R. Pennington, Young-Ki Paik, Christopher M. Overall, Fernando J. Corrales, Ileana M. Cristea, Jennifer E. Van Eyk, Mathias Uhlén (+34 others)
2020 Nature Communications  
On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint.  ...  The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate  ...  A full alphabetical listing of the Human Proteome Project members appears in the Supplementary Information.  ... 
doi:10.1038/s41467-020-19045-9 pmid:33067450 fatcat:eqth2b7nhfgsfmon7vdopgvlxq

Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach

Elizabeth Guruceaga, Alba Garin-Muga, Gorka Prieto, Bartolomé Bejarano, Miguel Marcilla, Consuelo Marín-Vicente, Yasset Perez-Riverol, J. Ignacio Casal, Juan Antonio Vizcaíno, Fernando J. Corrales, Victor Segura
2017 Journal of Proteome Research  
Finally, we performed a combined analysis of the gene expression levels and the proteomic identifications from the common cell lines between the NCI60 and the CCLE project to suggest alternatives for further  ...  Moreover, 165 missing proteins were detected with only one unique peptide and their functional analysis supported their participation in cellular pathways as was also proposed in other studies.  ...  Then, the neXtProt peptide uniqueness checker tool 15 was used to remove unique peptides that were considered ambiguous taking into account SNPs and disease mutations.  ... 
doi:10.1021/acs.jproteome.7b00388 pmid:28960077 pmcid:PMC5737412 fatcat:52yfuufhmfghhhg7xfmm3ilz3q

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, Yves Vandenbrouck, Ulrike Kusebauch, William S. Hancock, Henning Hermjakob (+3 others)
2016 Journal of Proteome Research  
Every data-rich community research effort requires a clear plan for ensuring the quality of the data interpretation and comparability of analyses.  ...  These guidelines, developed by the HPP community, are presented to the broader scientific community for further discussion.  ...  The authors have no conflicts of interest to declare. Supporting Information Supporting Information: Checklist document with extended description of the guidelines. Supplementary Document S1.  ... 
doi:10.1021/acs.jproteome.6b00392 pmid:27490519 pmcid:PMC5096969 fatcat:nyiuztfffvcpxiccn7ca4663hu

The Human Melanoma Proteome Atlas—Complementing the melanoma transcriptome

Lazaro Hiram Betancourt, Jeovanis Gil, Aniel Sanchez, Viktória Doma, Magdalena Kuras, Jimmy Rodriguez Murillo, Erika Velasquez, Uğur Çakır, Yonghyo Kim, Yutaka Sugihara, Indira Pla Parada, Beáta Szeitz (+45 others)
2021 Clinical and Translational Medicine  
The MM500 meta-study aims to establish a knowledge basis of the tumor proteome to serve as a complement to genome and transcriptome studies.  ...  By adding these key proteomic pillars, the MM500 study expands the knowledge on melanoma disease.  ...  Identification and sorting of unique peptides of missing proteins were carried using the neXtProt tool "Peptide uniqueness checker" (https://www.nextprot.org/tools/peptideuniqueness-checker).  ... 
doi:10.1002/ctm2.451 pmid:34323402 pmcid:PMC8299047 fatcat:27xtyjrziba7zhp3imsyrq22va

The human melanoma proteome atlas—Defining the molecular pathology

Lazaro Hiram Betancourt, Jeovanis Gil, Yonghyo Kim, Viktória Doma, Uğur Çakır, Aniel Sanchez, Jimmy Rodriguez Murillo, Magdalena Kuras, Indira Pla Parada, Yutaka Sugihara, Roger Appelqvist, Elisabet Wieslander (+45 others)
2021 Clinical and Translational Medicine  
The protein levels and localization were determined for a broad spectrum of diverse, surgically isolated melanoma tumors originating from multiple body locations.  ...  The data generated by global proteomic experiments covered 72% of the proteins identified in the recently reported high stringency blueprint of the human proteome.  ...  Identification and sorting of unique peptides were carried using the neXtProt tool "Peptide uniqueness checker" (https://www. nextprot.org/tools/peptide-uniqueness-checker).  ... 
doi:10.1002/ctm2.473 pmid:34323403 pmcid:PMC8255060 fatcat:mrym32vsi5ej7d5ucqqrijkjom

HBFP: a new repository for human body fluid proteome

Dan Shao, Lan Huang, Yan Wang, Xueteng Cui, Yufei Li, Yao Wang, Qin Ma, Wei Du, Juan Cui
2021
Body fluid proteome has been intensively studied as a primary source for disease biomarker discovery.  ...  As an important resource for human protein secretome, we anticipate that this new HBFP database can be a powerful tool that facilitates research in clinical proteomics and biomarker discovery.  ...  ., Daniel,T. et al. (2017) The neXtProt peptide uniqueness checker: a tool for the proteomics community. Bioinformatics, 33, 3471-3472. 18.  ... 
doi:10.1093/database/baab065 pmid:34642750 pmcid:PMC8516408 fatcat:qajcxm2pabajljlz6wvsqwxp44

Bioinformatics analysis of proteins and proteomes

Islam Mohammad
2022
However, the analysis and interpretation of this data remains a challenge, as several proteins remain unannotated and uncharacterised for many organisms.  ...  To this end, a scheme was worked out for comparing proteomics data from different sources, looking at proteotypicity and search engine scores, with guidelines on spectral quality analysis as well.  ...  Acknowledgements I am indebted to many individuals throughout my Ph.D. tenure for their assistance and support. The format of this thesis will not permit me to list every one of them.  ... 
doi:10.25949/19433357 fatcat:idrznpnkmfctfoxypc5cztsn3m
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