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ProMass for the Web – Help

Using ProMass for the Web
Getting there: The website for ProMass Online can be accessed here.
Setting up an account: You need to have an account to use the site. Click the “Sign Up” button at the top right of the web page and fill in requested information under “Create a ProMass account” to create your account. We’ll send a confirmation email to the email address you provide. You will then be able to sign in and start deconvoluting!

Feel free to contact us if you have any questions.

Deconvoluting your data (for new users):

  1. Novatia recommends starting on the “Deconvolution” tab with one of the predefined parameters sets, selecting the appropriate species of interest (oligo, peptide, small protein, large protein, and IgG).
  2. Most MS data systems have a way of exporting mass spectral data in text format (m/z, intensity) to the clipboard. Using the method appropriate for your data system, paste the spectrum into the proper field on the form or upload it as a “.txt” file.
  3. Click the “Run Deconvolution” button.
  4. When ProMass is done, the “Output” tab will show you your results. You should see:
    • Base Peak Mass (Da): The molecular mass for the major species in the spectrum in its uncharged state.
    • ESI Mass Spectrum: This is the graphical representation of the text data for the spectrum you entered earlier.
    • Deconvoluted Mass Spectrum: This is the zero-charge mass spectrum across the entire output mass range.
    • Zoom Display Deconvoluted Mass Spectrum: This is a detail of the mass range in which the major species falls.
    • Deconvoluted Peak Report: This is a tabular summary of the masses detected in the deconvoluted data with a variety of figures of merit.
    • The [View Data] web link will allow you to interactively zoom the spectra or show the charge series for any deconvoluted masses.
  5. Unexpected results?
    • Check that the “Input m/z range” field covers the region of the mass spectrum
      where all of your multiply charged peaks reside
    • Check that the “Output mass range” is reasonable for your species of interest.
      For example, if you have a textbook electrospray spectrum but see at least two output peaks with widely differing masses, you may need to expand your output mass range.
    • Check that the “Polarity” is appropriate for your data.  If your data was acquired in positive ion mode select positive [+] polarity.  If your data was acquired in negative ion mode, select negative [-] ion mode.  If you select the wrong polarity, your deconvoluted masses will not be accurate.
    • If you observe a timeout error on the server, please delete any header information from either data pasted from clipboard or the data file header in the text file itself, so that the only data uploaded to ProMass is the list of mass/intensity pairs. Give ProMass numbers only.
      Email for more detailed assistance.