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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 one spectra at a time cumbersome. Here we provide a method to batch upload many spectra.

Here is a quick instructional video we have put together:


The materials that are required are:

  1. Annotation Spread Sheet (This can be produced below manually by selecting scans in the mass spec data, or automatically generated with the MSMS-Chooser workflow - see documentation)
  2. Source mzXML/mzML/mgf mass spectra files to pull MS/MS spectra

ATTENTION: Batch Annotation Workflow should be used to create spectral libraries of 50 spectra or more. Please contact CCMS Team with questions (

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, or deleted or changed. Each column must have a value. Refer to the table below for default values to enter when not known.

Export from this Excel file as a tab separated text file (recommended export from Windows office 2013 or newer. Verify that line endings are UNIX and not Windows line endings).

Batch File Annotation

To check the validity of your batch file, check out our batch validator.

Field Information

The field requirements are the same as on the single spectrum upload form, the 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, mzML, or mgf) REQUIRED only letters, numbers, underscores and periods are allowed Yes
SEQ Peptide Sequence *..* Please enter *..* here only No
MOLECULEMASS Corrected Precursor MZ for Compound 0 Entering 0 means we will attempt to read the mz value from file No
INSTRUMENT Mass Analyzer Instrument REQUIRED qTof, QQQ, Ion Trap, Hybrid FT, Orbitrap, ToF Yes
EXTRACTSCAN Spectrum Scan of Spectrum REQUIRED Yes
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 the 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 REQUIRED Yes
ADDUCT Adduct of Ion Fragmented in MS2 (M+H, M+2H, etc.) REQUIRED Yes
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 N/A No
PI PI overseeing compound acquisition and analysis Required Yes

It must be noted that filenames must match exactly to those users are uploading. Filenames 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 or tabs.

Spectrum Upload

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

Creation/Publication of Spectral Library

To actually add the spectra to the libraries, users will

  1. Export excel file as a tab separated text file and upload to GNPS (recommended export from Windows office 2013 or newer. Verify that line endings are UNIX and not Windows line endings)
  2. Launch Batch Validator Workflow with all spectrum files and annotation table found here. NOTE: Creating spectral libraries from MGF files is discouragedas it is not a well defined format. If you do insist, you must make sure each MGF start from scan 1 (e.g. SCANS=1 in the file) and are incremented sequentially without any missing scan numbers.
  3. Users will then need to contact the Wang Bioninformatics Lab ( and send her the completed job from above.
  4. A private spectral library will then be created by Jasmine.
  5. After the contributor may review the library to be made into a public library and will be made public after approval.


All GNPS Reference spectra contributed directly to GNPS by default will have the CC0 license.

Third party libraries imported may not conform to the CC BY license and should be verified by users.

Page Contributions

Ming Wang (40.45%), mpanitch (58.43%), klj0019 (1.12%)

Last update: April 18, 2024 22:25:46