Added by Mingxun Wang, last edited by Mingxun Wang on Feb 28, 2017  (view change)


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Batch Upload of Annotated Spectra

While there is an interface to upload single spectra, users who wish to batch upload many spectra into the libraries might find adding spectra one at a time cumbersome. Here we provide a method to batch upload many spectra.

Annotation Spread Sheet

To batch upload, this template must be used:

Template Spreadsheet

Annotation are to be added one spectrum per line.  Columns may not be added, deleted or changed. Each column must have a value. Refer to the table below for default values to enter when not known. 

Field Information

The field requirements are the same as on the single spectrum upload form, other columns can be ignored. Field description are listed below.

Please note: Only letters, numbers and underscores are allowed in the filenames.  Spaces and special characters are NOT allowed.

Header Desc. Default Value To Put When Not Known Possible Values Required
FILENAME Input Filename (mzXML) REQUIRED only letters numbers underscores and periods are allowed Yes
SEQ Peptide Sequence *..*   No
COMPOUND_NAME Compound Common Name
MOLECULEMASS Corrected Precursor MZ for Compound
0   No
INSTRUMENT Mass Analyzer Instrument
qTof, QQQ, Ion Trap, Hybrid FT, Orbitrap Yes
IONSOURCE Source of Ions
EXTRACTSCAN Spectrum Scan of Spectrum
SMILES Smiles Structure
N/A   No
INCHI Inchi Structure
N/A   No
INCHIAUX Inchi Auxiliary Structure
N/A   No
CHARGE Charge of Precursor (0 to pull from spectrum file)
0   No
IONMODE Ionization Mode (Positive/Negative)
Positive Positive, Negative Yes
PUBMED Pubmed ID where compound or data was published
N/A   No
ACQUISITION Sample source of compound
Crude Crude, Lysate, Commercial, Isolated, Other Yes
EXACTMASS Compound Exact Mass
0   No
DATACOLLECTOR Individual collecting data
ADDUCT Adduct of Ion fragmented in MS2 (M+H, M+2H, etc.)
LIBQUALITY Quality of Library (1 for Gold, 2 for Silver, 3 for Bronze) 3 1,2,3 Yes
GENUS Genus N/A   No
SPECIES Species N/A   No
STRAIN Strain N/A   No
CASNUMBER Chemical Abstracts Service compound identification number
PI PI overseeing compound acquisition and analysis

It must be noted that filenames must match exactly to those users are uploading. File names must also be unique, and can only contain numbers, letters, hyphens, underscores, and periods. All fields for each row must have some content, blank fields are unacceptable. Fields other than filename also cannot contain return carriages, spaces, or tabs.

Spectrum upload

Users will need to upload their files into gnps. To do this please refer to the upload documentation here.

Spectrum Addition to Library

To actually add the spectra to the libraries, users will

  1. Need to upload an empty mgf file to GNPS so that it appears in the file selector directory. 
  2. Export excel file as a tab separated text file and uploaded to GNPS (recommended export form Windows office 2013 or newer. Verify that line endings are UNIX and not Windows line endings)
  3. Users will then need to click here to utilize the batch workflow and select the mgf file created to hold the library, the input spectrum files, and the text version of the annotations. Addendum: Access to workflow is restricted - To request access please email Ming (
  4. After the workflow completes, the mgf file will now be populated with the batch uploaded spectra.
  5. To contribute this library to the public GNPS library, please email Ming (, listing the location of the library and the public library it should be added to for approval.