Mass Spectrometry Virtual Interactive Environment

Abbreviation:MassIVE

Recommended

General Information

MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange accessions to satisfy publication requirements.

Homepage https://massive.ucsd.edu

Countries that developed this resource United States

Created in 2012

Taxonomic range

All

Knowledge Domains

Subjects

In the following recommendations:

Scientific Data

How to cite this record FAIRsharing.org: MassIVE; Mass Spectrometry Virtual Interactive Environment; DOI: https://doi.org/10.25504/FAIRsharing.LYsiMd; Last edited: March 29, 2021, 11:03 a.m.; Last accessed: May 18 2021 6:51 a.m.

This record is maintained by mwang87

Record added: Aug. 29, 2018, 7:39 p.m.
Record updated: March 29, 2021, 10:51 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.LYsiMd' by 'The FAIRsharing Team' at 10:51, 29 Mar 2021 (approved):

	'supportLinks' has been modified:
		Before:
			email|ccms-web@cs.ucsd.edu
			help|https://massive.ucsd.edu/ProteoSAFe/help.jsp
			help|https://massive.ucsd.edu/ProteoSAFe/demo_2.jsp
		After:
			email|ccms-web@cs.ucsd.edu
			help|https://massive.ucsd.edu/ProteoSAFe/help.jsp
			help|https://massive.ucsd.edu/ProteoSAFe/demo_2.jsp
			online documentation|https://ccms-ucsd.github.io/MassIVEDocumentation
		Added:
			online documentation|https://ccms-ucsd.github.io/MassIVEDocumentation
		Removed:

	'accessPoints' has been modified:
		Before:
		After:
			REST|https://ccms-ucsd.github.io/MassIVEDocumentation/#api/|API Documentation
		Added:
			REST|https://ccms-ucsd.github.io/MassIVEDocumentation/#api/|API Documentation
		Removed:

	'tools' has been modified:
		Before:
			Reanalyze Spectra||http://proteomics.ucsd.edu/service/massive/documentation/reanalyze-spectra/
			Protein Explorer (beta)||https://massive.ucsd.edu/ProteoSAFe/protein_explorer_splash.jsp
			Results Comparison||http://proteomics2.ucsd.edu/ProteoSAFe/index.jsp?params=%7B%22workflow%22:%22SERVERSIDE_RESULTS_COMPARISON_INPUT_INTEGRATED%22,%22library_on_server%22:%22d.speclibs;%22%7D
		After:
		Added:
		Removed:
			Reanalyze Spectra||http://proteomics.ucsd.edu/service/massive/documentation/reanalyze-spectra/
			Protein Explorer (beta)||https://massive.ucsd.edu/ProteoSAFe/protein_explorer_splash.jsp
			Results Comparison||http://proteomics2.ucsd.edu/ProteoSAFe/index.jsp?params=%7B%22workflow%22:%22SERVERSIDE_RESULTS_COMPARISON_INPUT_INTEGRATED%22,%22library_on_server%22:%22d.speclibs;%22%7D

	'dataProcesses' has been modified:
		Before:
			Submit Data, data curation, http://proteomics.ucsd.edu/service/massive/documentation/submit-data/
			Browse Data, data access, https://massive.ucsd.edu/ProteoSAFe/datasets.jsp#%7B%22query%22%3A%7B%7D%2C%22table_sort_history%22%3A%22createdMillis_dsc%22%7D
			Submit Reanalyses, data curation, http://proteomics.ucsd.edu/service/massive/documentation/share-reanalyses/
		After:
			Submit Data, data curation, http://proteomics.ucsd.edu/service/massive/documentation/submit-data/
			Browse Data, data access, https://massive.ucsd.edu/ProteoSAFe/datasets.jsp#%7B%22query%22%3A%7B%7D%2C%22table_sort_history%22%3A%22createdMillis_dsc%22%7D
			Submit Reanalyses, data curation, http://proteomics.ucsd.edu/service/massive/documentation/share-reanalyses/
			Search, data access, https://massive.ucsd.edu/ProteoSAFe/massive_search.jsp
			Reanalyse Data, data access, https://ccms-ucsd.github.io/MassIVEDocumentation/reanalyze_spectra/
			MassIVE Knowledgebase, data access, https://massive.ucsd.edu/ProteoSAFe/static/massive-kb-libraries.jsp
			Protein Explorer, data access, https://massive.ucsd.edu/ProteoSAFe/protein_explorer_splash.jsp
			MassIVE.Quant, data access, https://massive.ucsd.edu/ProteoSAFe/static/massive-quant.jsp
			CoronaMassKB, data access, https://massive.ucsd.edu/ProteoSAFe/static/corona-mass-kb.jsp
		Added:
			Search, data access, https://massive.ucsd.edu/ProteoSAFe/massive_search.jsp
			Reanalyse Data, data access, https://ccms-ucsd.github.io/MassIVEDocumentation/reanalyze_spectra/
			MassIVE Knowledgebase, data access, https://massive.ucsd.edu/ProteoSAFe/static/massive-kb-libraries.jsp
			Protein Explorer, data access, https://massive.ucsd.edu/ProteoSAFe/protein_explorer_splash.jsp
			MassIVE.Quant, data access, https://massive.ucsd.edu/ProteoSAFe/static/massive-quant.jsp
			CoronaMassKB, data access, https://massive.ucsd.edu/ProteoSAFe/static/corona-mass-kb.jsp
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.LYsiMd' by 'The FAIRsharing Team' at 10:46, 29 Mar 2021 (approved):

	'onto_disciplines' has been modified:
		Before:
			Life Science
			Metabolomics
			Proteomics
		After:
			Metabolomics
			Proteomics
			Transcriptomics
		Added:
			Transcriptomics
		Removed:
			Life Science

	'dataProcesses' has been modified:
		Before:
			Deposition Documentation, data access, http://proteomics.ucsd.edu/service/massive/documentation/submit-data/
			Browse Data, data access, https://massive.ucsd.edu/ProteoSAFe/datasets.jsp#%7B%22query%22%3A%7B%7D%2C%22table_sort_history%22%3A%22createdMillis_dsc%22%7D
			Share / Upload Results, data curation, http://proteomics.ucsd.edu/service/massive/documentation/share-reanalyses/
		After:
			Submit Data, data curation, http://proteomics.ucsd.edu/service/massive/documentation/submit-data/
			Browse Data, data access, https://massive.ucsd.edu/ProteoSAFe/datasets.jsp#%7B%22query%22%3A%7B%7D%2C%22table_sort_history%22%3A%22createdMillis_dsc%22%7D
			Submit Reanalyses, data curation, http://proteomics.ucsd.edu/service/massive/documentation/share-reanalyses/
		Added:
			Submit Data, data curation, http://proteomics.ucsd.edu/service/massive/documentation/submit-data/
			Submit Reanalyses, data curation, http://proteomics.ucsd.edu/service/massive/documentation/share-reanalyses/
		Removed:
			Deposition Documentation, data access, http://proteomics.ucsd.edu/service/massive/documentation/submit-data/
			Share / Upload Results, data curation, http://proteomics.ucsd.edu/service/massive/documentation/share-reanalyses/

	'homepage' has been modified:
		Before: https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp
		After: https://massive.ucsd.edu

	'publications' has been modified:
		Before:
			The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.|Deutsch EW,Csordas A,Sun Z,Jarnuczak A,Perez-Riverol Y,Ternent T,Campbell DS,Bernal-Llinares M,Okuda S,Kawano S,Moritz RL,Carver JJ,Wang M,Ishihama Y,Bandeira N,Hermjakob H,Vizcaino JA|Nucleic Acids Res|2016
			Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.|Wang M,Carver JJ,Phelan VV,Sanchez LM,Garg N,Peng Y,Nguyen DD,Watrous J,Kapono CA,Luzzatto-Knaan T,Porto C,Bouslimani A,Melnik AV,Meehan MJ,Liu WT,Crusemann M,Boudreau PD,Esquenazi E,Sandoval-Calderon M,Kersten RD,Pace LA,Quinn RA,Duncan KR,Hsu CC,Floros DJ,Gavilan RG,Kleigrewe K,Northen T,Dutton RJ,Parrot D,Carlson EE,Aigle B,Michelsen CF,Jelsbak L,Sohlenkamp C,Pevzner P,Edlund A,McLean J,Piel J,Murphy BT,Gerwick L,Liaw CC,Yang YL,Humpf HU,Maansson M,Keyzers RA,Sims AC,Johnson AR,Sidebottom AM,Sedio BE,Klitgaard A,Larson CB,P CAB,Torres-Mendoza D,Gonzalez DJ,Silva DB,Marques LM,Demarque DP,Pociute E,O'Neill EC,Briand E,Helfrich EJN,Granatosky EA,Glukhov E,Ryffel F,Houson H,Mohimani H,Kharbush JJ,Zeng Y,Vorholt JA,Kurita KL,Charusanti P,McPhail KL,Nielsen KF,Vuong L,Elfeki M,Traxler MF,Engene N,Koyama N,Vining OB,Baric R,Silva RR,Mascuch SJ,Tomasi S,Jenkins S,Macherla V,Hoffman T,Agarwal V,Williams PG,Dai J,Neupane R,Gurr J,Rodriguez AMC,Lamsa A,Zhang C,Dorrestein K,Duggan BM,Almaliti J,Allard PM,Phapale P,Nothias LF,Alexandrov T,Litaudon M,Wolfender JL,Kyle JE,Metz TO,Peryea T,Nguyen DT,VanLeer D,Shinn P,Jadhav A,Muller R,Waters KM,Shi W,Liu X,Zhang L,Knight R,Jensen PR,Palsson BO,Pogliano K,Linington RG,Gutierrez M,Lopes NP,Gerwick WH,Moore BS,Dorrestein PC,Bandeira N|Nat Biotechnol|2016
		After:
			The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.|Deutsch EW,Csordas A,Sun Z,Jarnuczak A,Perez-Riverol Y,Ternent T,Campbell DS,Bernal-Llinares M,Okuda S,Kawano S,Moritz RL,Carver JJ,Wang M,Ishihama Y,Bandeira N,Hermjakob H,Vizcaino JA|Nucleic Acids Res|2016
			Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.|Wang M,Carver JJ,Phelan VV et al.|Nat Biotechnol|2016
			MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets.|Choi M,Carver J,Chiva C,Tzouros M,Huang T,Tsai TH,Pullman B,Bernhardt OM,Huttenhain R,Teo GC,Perez-Riverol Y,Muntel J,Muller M,Goetze S,Pavlou M,Verschueren E,Wollscheid B,Nesvizhskii AI,Reiter L,Dunkley T,Sabido E,Bandeira N,Vitek O|Nat Methods|2020
			The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.|Deutsch EW,Bandeira N,Sharma V,Perez-Riverol Y,Carver JJ,Kundu DJ,Garcia-Seisdedos D,Jarnuczak AF,Hewapathirana S,Pullman BS,Wertz J,Sun Z,Kawano S,Okuda S,Watanabe Y,Hermjakob H,MacLean B,MacCoss MJ,Zhu Y,Ishihama Y,Vizcaino JA|Nucleic Acids Res|2019
		Added:
			Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.|Wang M,Carver JJ,Phelan VV et al.|Nat Biotechnol|2016
			MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets.|Choi M,Carver J,Chiva C,Tzouros M,Huang T,Tsai TH,Pullman B,Bernhardt OM,Huttenhain R,Teo GC,Perez-Riverol Y,Muntel J,Muller M,Goetze S,Pavlou M,Verschueren E,Wollscheid B,Nesvizhskii AI,Reiter L,Dunkley T,Sabido E,Bandeira N,Vitek O|Nat Methods|2020
			The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.|Deutsch EW,Bandeira N,Sharma V,Perez-Riverol Y,Carver JJ,Kundu DJ,Garcia-Seisdedos D,Jarnuczak AF,Hewapathirana S,Pullman BS,Wertz J,Sun Z,Kawano S,Okuda S,Watanabe Y,Hermjakob H,MacLean B,MacCoss MJ,Zhu Y,Ishihama Y,Vizcaino JA|Nucleic Acids Res|2019
		Removed:
			Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.|Wang M,Carver JJ,Phelan VV,Sanchez LM,Garg N,Peng Y,Nguyen DD,Watrous J,Kapono CA,Luzzatto-Knaan T,Porto C,Bouslimani A,Melnik AV,Meehan MJ,Liu WT,Crusemann M,Boudreau PD,Esquenazi E,Sandoval-Calderon M,Kersten RD,Pace LA,Quinn RA,Duncan KR,Hsu CC,Floros DJ,Gavilan RG,Kleigrewe K,Northen T,Dutton RJ,Parrot D,Carlson EE,Aigle B,Michelsen CF,Jelsbak L,Sohlenkamp C,Pevzner P,Edlund A,McLean J,Piel J,Murphy BT,Gerwick L,Liaw CC,Yang YL,Humpf HU,Maansson M,Keyzers RA,Sims AC,Johnson AR,Sidebottom AM,Sedio BE,Klitgaard A,Larson CB,P CAB,Torres-Mendoza D,Gonzalez DJ,Silva DB,Marques LM,Demarque DP,Pociute E,O'Neill EC,Briand E,Helfrich EJN,Granatosky EA,Glukhov E,Ryffel F,Houson H,Mohimani H,Kharbush JJ,Zeng Y,Vorholt JA,Kurita KL,Charusanti P,McPhail KL,Nielsen KF,Vuong L,Elfeki M,Traxler MF,Engene N,Koyama N,Vining OB,Baric R,Silva RR,Mascuch SJ,Tomasi S,Jenkins S,Macherla V,Hoffman T,Agarwal V,Williams PG,Dai J,Neupane R,Gurr J,Rodriguez AMC,Lamsa A,Zhang C,Dorrestein K,Duggan BM,Almaliti J,Allard PM,Phapale P,Nothias LF,Alexandrov T,Litaudon M,Wolfender JL,Kyle JE,Metz TO,Peryea T,Nguyen DT,VanLeer D,Shinn P,Jadhav A,Muller R,Waters KM,Shi W,Liu X,Zhang L,Knight R,Jensen PR,Palsson BO,Pogliano K,Linington RG,Gutierrez M,Lopes NP,Gerwick WH,Moore BS,Dorrestein PC,Bandeira N|Nat Biotechnol|2016

	'onto_domains' has been modified:
		Before:
			Mass spectrometry spectra
			Natural Product
		After:
			Gene expression data
			Mass spectrometry spectra
			protocol
			study design
		Added:
			Gene expression data
			protocol
			study design
		Removed:
			Natural Product

Edits to 'https://fairsharing.org/FAIRsharing.LYsiMd' by 'The FAIRsharing Team' at 14:21, 16 Oct 2018 (approved):

	'organizations' has been modified:
		Before:
			NIGMS|http://www.nigms.nih.gov|Funds
		After:
			NIGMS|http://www.nigms.nih.gov|Funds
			Center for Computational Mass Spectrometry, University of California San Diego, United States|http://proteomics.ucsd.edu/|Maintains
		Added:
			Center for Computational Mass Spectrometry, University of California San Diego, United States|http://proteomics.ucsd.edu/|Maintains
		Removed:

	'related_databases' has been modified:
		Before:
			PRoteomics IDEntifications database
			Japan Proteome Standard Repository
		After:
			PRoteomics IDEntifications database
			ProteomeXchange
			Japan Proteome Standard Repository
		Added:
			ProteomeXchange
		Removed:

	'tools' has been modified:
		Before:
			Reanalyze Spectra||http://proteomics.ucsd.edu/service/massive/documentation/reanalyze-spectra/
		After:
			Reanalyze Spectra||http://proteomics.ucsd.edu/service/massive/documentation/reanalyze-spectra/
			Protein Explorer (beta)||https://massive.ucsd.edu/ProteoSAFe/protein_explorer_splash.jsp
			Results Comparison||http://proteomics2.ucsd.edu/ProteoSAFe/index.jsp?params=%7B%22workflow%22:%22SERVERSIDE_RESULTS_COMPARISON_INPUT_INTEGRATED%22,%22library_on_server%22:%22d.speclibs;%22%7D
		Added:
			Protein Explorer (beta)||https://massive.ucsd.edu/ProteoSAFe/protein_explorer_splash.jsp
			Results Comparison||http://proteomics2.ucsd.edu/ProteoSAFe/index.jsp?params=%7B%22workflow%22:%22SERVERSIDE_RESULTS_COMPARISON_INPUT_INTEGRATED%22,%22library_on_server%22:%22d.speclibs;%22%7D
		Removed:

	'dataProcesses' has been modified:
		Before:
			Deposition Documentation
			Browse Data
		After:
			Deposition Documentation
			Browse Data
			Share / Upload Results
		Added:
			Share / Upload Results
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.LYsiMd' by 'The FAIRsharing Team' at 11:03, 06 Sep 2018 (approved):

	'domains' has been modified:
		Before:
			Mass spectrometry spectra
			Metabolomics
			Natural products
			Proteomics
		After:
			Life Science
			Mass spectrometry spectra
			Metabolomics
			Natural products
			Proteomics
		Added:
			Life Science
		Removed:

	'supportLinks' has been modified:
		Before:
		After:
			email|ccms-web@cs.ucsd.edu
			help|https://massive.ucsd.edu/ProteoSAFe/help.jsp
			help|https://massive.ucsd.edu/ProteoSAFe/demo_2.jsp
		Added:
			email|ccms-web@cs.ucsd.edu
			help|https://massive.ucsd.edu/ProteoSAFe/help.jsp
			help|https://massive.ucsd.edu/ProteoSAFe/demo_2.jsp
		Removed:

	'taxonomies' has been modified:
		Before:
		After:
			All
		Added:
			All
		Removed:

	'tools' has been modified:
		Before:
		After:
			Reanalyze Spectra||http://proteomics.ucsd.edu/service/massive/documentation/reanalyze-spectra/
		Added:
			Reanalyze Spectra||http://proteomics.ucsd.edu/service/massive/documentation/reanalyze-spectra/
		Removed:

	'dataProcesses' has been modified:
		Before:
			Deposition Documentation
		After:
			Deposition Documentation
			Browse Data
		Added:
			Browse Data
		Removed:

Support

General

support email	General Support
help	General Information
help	InsPecT Demonstration Video and Results
online documentation	General Documentation

Additional Information

Contact

Mingxun Wang ORCID

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication

Data Curation

Submit Data	http://proteomics.ucsd.edu/service/massive/documentation/submit-data/
Submit Reanalyses	http://proteomics.ucsd.edu/service/massive/documentation/share-reanaly ...

Data Access

Browse Data	https://massive.ucsd.edu/ProteoSAFe/datasets.jsp#%7B%22query%22%3A%7B% ...
Search	https://massive.ucsd.edu/ProteoSAFe/massive_search.jsp
Reanalyse Data	https://ccms-ucsd.github.io/MassIVEDocumentation/reanalyze_spectra/
MassIVE Knowledgebase	https://massive.ucsd.edu/ProteoSAFe/static/massive-kb-libraries.jsp
Protein Explorer	https://massive.ucsd.edu/ProteoSAFe/protein_explorer_splash.jsp
MassIVE.Quant	https://massive.ucsd.edu/ProteoSAFe/static/massive-quant.jsp
CoronaMassKB	https://massive.ucsd.edu/ProteoSAFe/static/corona-mass-kb.jsp

REST Web Services

API Documentation

https://ccms-ucsd.github.io/MassIVEDocumentation/#api/

Publications

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.

Deutsch EW,Csordas A,Sun Z,Jarnuczak A,Perez-Riverol Y,Ternent T,Campbell DS,Bernal-Llinares M,Okuda S,Kawano S,Moritz RL,Carver JJ,Wang M,Ishihama Y,Bandeira N,Hermjakob H,Vizcaino JA
Nucleic Acids Res 2016

View Paper (PubMed) View Publication

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Wang M,Carver JJ,Phelan VV et al.
Nat Biotechnol 2016

View Paper (PubMed) View Publication

MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets.

Choi M,Carver J,Chiva C,Tzouros M,Huang T,Tsai TH,Pullman B,Bernhardt OM,Huttenhain R,Teo GC,Perez-Riverol Y,Muntel J,Muller M,Goetze S,Pavlou M,Verschueren E,Wollscheid B,Nesvizhskii AI,Reiter L,Dunkley T,Sabido E,Bandeira N,Vitek O
Nat Methods 2020

View Paper (PubMed) View Publication

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.

Deutsch EW,Bandeira N,Sharma V,Perez-Riverol Y,Carver JJ,Kundu DJ,Garcia-Seisdedos D,Jarnuczak AF,Hewapathirana S,Pullman BS,Wertz J,Sun Z,Kawano S,Okuda S,Watanabe Y,Hermjakob H,MacLean B,MacCoss MJ,Zhu Y,Ishihama Y,Vizcaino JA
Nucleic Acids Res 2019

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

Scientific Data Data Policy

Credit

Record Maintainer

This record is maintained by mwang87

Funds

National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA (Government body)

Maintains

Center for Computational Mass Spectrometry, University of California San Diego, United States (Research institute) Lead

Grant Number(s)

5P41GM103484-09 (National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA)

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