FAQ


Who can submit data to vMS-Share?

Interested parties should provide a link (eg.cloud bucket link) from which we can download / access their data. Currently, direct data deposition is not availabe but we are working on implementing that feature in the near future.


What is the format in which to submit data to vMS-Share?

Data input pipeline for vMS-Share requires two files:

      1) Raw data file. The following data formats are accepted:
             a) Agilent MassHunter .d
             b) Applied Biosystems WIFF
             b) Bruker Compass .d, FID/YEP/BAF
             c) Thermo RAW
             d) Waters MassLynx .raw

      2) Flat text file with tab separated values (TSV) containing the following column order:

             Proteomics
             a) RAW file name of a given peptide identification
             b) Scan number (Scan ID from the RAW file)
             c) Retention time rounded to 4 decimal places
             d) Corresponding peptide sequence
             e) Precursor m/z [Da]
             f) MH+ [Da]
             g) DM [ppm]
             h) Charge
             i) Confidence score (e.g. Xcorr)
             j) #PSMs
             k) Modifications
             l) Protein accession number
             m) Protein name
             n) Protein reference number (optional)
             o) Corresponding gene name (optional)


             Metabolomics
             a) RAW file name of a given metabolite identification
             b) Scan number (Scan ID from the RAW file)
             c) Retention time rounded to 4 decimal places
             d) Corresponding metabolite name
             e) Formula
             f) Score
             g) MS1 Precursor m/z
             h) MS1 Total Intensity (optional)
             i) MS1 Total Abundance (optional)
             j) Precursor Type (optional)
             k) CAS Number (optional)
             l) Charge (optional)
             m) Instrument Type (optional)
             n) Library Name (optional)
             o) Area (Max.) (optional)


What type of mass spectra can be displayed on vMS-Share?

LC/MS and GC/MS data can be displayed on vMS-Share.


What type of data is vMS-Share able to share?

vMS-Share is designed to serve as a hub for sharing Metabolomic, Proteomic, Lipidomic and Standard Reference Material (SRM) data.