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MassIVE Data Repository

MassIVE is an online repository for publicly available datasets. MassIVE provides a location for researchers to access datasets that have been made available by others, oftentimes alongside publication. The datasets available remain alive long after publication. At GNPS, users will be able to browse datasets, download datasets, and comment on datasets. These comments can be accompanied with new data or new analysis that enriches the MassIVE dataset. Additionally, users can subscribe to specific datasets. While the underlying data may not change, the analysis and understanding of the data will continue to improve. To enhance the analysis, datasets submitted to MassIVE through GNPS will be periodically searched against the ever growing annotated spectral libraries and new putative identifications within those datasets are reported to subscribers. Beyond new identifications within a dataset, subscribers will also be made aware of other datasets that exhibit chemical similarities to the subscribed dataset. This allows for users to be connected via their research interest to similar datasets.

Here we will describe how to upload data into MassIVE specifically for GNPS.

For more detailed information about general MassIVE dataset submission see here .

GNPS MassIVE Submissions

Acceptable File Inputs

MassIVE datasets are composed of data files. Acceptable input files are as follows:

Vendor Preferred Format Comment
Bruker mzXML Centroided MS1 and MS2
Thermo RAW, mzXML  
Agilent mzXML  
AB Sciex WIFF, mzXML  

NOTE: We do not support file archives of data files (e.g. zip, tar). Data files must be submitted as the naked file and not in an archive.

File Upload to MassIVE servers

The preferred method to upload data is through FTP. The ftp server is at massive.ucsd.edu and please refer to documentation here .

MassIVE Dataset Submission

At the GNPS splash screen, users can click this icon

to create a MassIVE dataset.

Login with your GNPS login and hit Submit Data.

Further instructions can be found here.

GNPS Submission specifics

The title is the display that users will use primarily to filter datasets. For GNPS datasets, a specific title format is required.

 GNPS - <Title of Paper or Short Description>

The GNPS prefix is required for GNPS datasets. If this is not provided GNPS MassIVE datasets are not shown to GNPS users. 

Example Recommended Description

Paper title: Molecular networking as a dereplication strategy.
Author List: Yang JY, Sanchez LM, Rath CM, Liu X, Boudreau PD, Bruns N, Glukhov E, Wodtke A, de Felicio R, Fenner A, Wong WR, Linington RG, Zhang L, Debonsi HM, Gerwick WH, Dorrestein PC.
Citation: J Nat Prod. 2013 Sep 27;76(9):1686-99. doi: 10.1021/np400413s
PubMedID: 24025162
Brief description of the data submitted: RAW Files used to generate Figure 4. Bacterial network with a cosine similarity score cutoff of 0.65. This network was generated from direct infusion of extracts or direct

Checking Submission

Publicly available GNPS MassIVE datasets can be viewed here.

Known MassIVE issues

FTP connections to massive.ucsd.edu might fail on new accounts. To work around this bug, please go to massive.ucsd.edu/ProteoSAFe and click Select Input Files. This will bring a popup, now try to again connect via FTP, if the problem persists, please email miw023@cs.ucsd.edu.