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.
To batch upload, this template must be used:
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.
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|
|COMPOUND_NAME|| Compound Common Name
|MOLECULEMASS|| Corrected Precursor MZ for Compound
|INSTRUMENT|| Mass Analyzer Instrument
||qTof, QQQ, Ion Trap, Hybrid FT, Orbitrap||Yes|
|IONSOURCE|| Source of Ions
|EXTRACTSCAN|| Spectrum Scan of Spectrum
|SMILES|| Smiles Structure
|INCHI|| Inchi Structure
|INCHIAUX|| Inchi Auxiliary Structure
|CHARGE|| Charge of Precursor (0 to pull from spectrum file)
|IONMODE|| Ionization Mode (Positive/Negative)
|PUBMED|| Pubmed ID where compound or data was published
|ACQUISITION|| Sample source of compound
||Crude||Crude, Lysate, Commercial, Isolated, Other||Yes|
|EXACTMASS|| Compound Exact Mass
|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|
|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.
Users will need to upload their files into gnps. To do this please refer to the upload documentation here.
To actually add the spectra to the libraries, users will
- Need to upload an empty mgf file to GNPS so that it appears in the file selector directory.
- 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)
- 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 (firstname.lastname@example.org)
- After the workflow completes, the mgf file will now be populated with the batch uploaded spectra.
- To contribute this library to the public GNPS library, please email Ming (email@example.com), listing the location of the library and the public library it should be added to for approval.