Since 10 years now, our group is developing multiple routine applications for any kind of mass spectrometry calculations. In this page you will find basic applications such as our molecular mass calculator to generate monoisotopic mass of any molecular formula or our molecular formula calculator to find possible molecular formula based on your experimental value. You can also generate all possible fragments and combine them in our fragmentation tool. Finally, you could use our modification tool for proteins, based on the Unimod database, for your proteomics research
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Generate theoretical isotopic distributions for any molecule and different ionization adducts.
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Generate possible molecular formula for your experimental peak. Look at the possible corresponding compounds directly in Pubchem.
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Generate possible molecular formula for your experimental peak and select elements based on their specific isotopic distribution.
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Search protein modifications by monoisotopic mass, amino acid or name. This tool uses the UNIMOD database.
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Draw/import a structure, cut it and generate a list of fragments that can all be combined.
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Find out another open access applications for DNA/RNA data interpretation
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Application tips

for our Mass Spectrometry calculators

Tool 1

This tool allows calculating the theoretical isotopic distribution and monoisotopic mass from a Molecular Formula. It is possible to  indicate predefined groups, chemical modification of amino acids, specify a given isotope, and modify the isotopic abundance. You can draw the structure or edit directly the molecular formula. Take a few minutes to read these useful tips:

  • You can use any atom or group of atoms separated by a comma “,”
  • Check our predefined group list and use it directly in the molecular formula by clicking on the little grid icon.
  • Use specific isotopes.
  • Use specific isotope abundances.
  • Specify ionization, charges and adducts. You can use several charges separated by a comma “,”
  • Define any chemical modification of any predefined group.
  • Define your FWHM for a profile spectrum (for small FWHM values click on Predict mass spectra).
  • Experimental data can be pasted and overlaid with the calculated distribution within mass spectra window but no similarity scores are provided here.
  • The content of this window can be either printed or exported as SVG file (option bar).

Tool 2

This tool allows finding possible molecular formula for a measured monoisotopic mass. Just remember that the monoisotopic mass is not always neither the most abundant peak of the isotopic distribution nor the one with the lowest mass.

  • First write the target observed monoisotopic mass.
  • Specify charges and adduts for ionization. You can use several charges separated by a comma “,”
  • Define the range of atoms that should be explored.
  • Define the mass tolerance in ppm.
  • Use the unsaturation filters if needed.
  • Define the FWHM (0 for centroid spectum)
  • The list of possible molecular formula will be displayed. Possible corresponding structures published in Pubchem highlighted in green can be viewed by clicking on the database icon.
  • You can compare different isotopic distributions (custom, clicked and hover structures).
  • Experimental data can be pasted and overlaid with the calculated distribution within mass spectra window but no similarity scores are given here.
  • The content of this window can be either printed or exported as SVG file (option bar).

Tool 3

Advanced molecular formula calculator

This tool allows to find possible molecular formula based on a molecular formula range like the tool 2. As in tool 2, any atom can be specified from the “Atom range selector” table. The main difference is that this atom range selector assists in the selection of the elements, the following information are displayed for each element.  This is especially useful for complicated unknown isotopic distributions. Sarch in our glossary the atom range selector definitions. For further explanations, check the Molecular formula from monoisotopic mass calculator (tool 2) in this page. Consult as tutorial the halogen example (click on Load).

Tool 4

Protein modification calculator

This tool allows a quick search in the UNIMOD database. This application permits to combine three easy types of searches:

  • Search my monoisotopic mass (with the specified precision in ppm)
  • Search by amino acids that can be modified
  • Search by the modification name by typing directly the name in the window of the list of matching entries.

Tool 5

Fragment generator

This tool generates a list of possible MS/MS fragments for small molecules. It is particularly useful for automatic calculation of electron impact fragments.

  • Draw your molecule in the edit window
  • Select the bonds that you want to cleave with the blue circle icon. It will generate the direct fragment ions and all possible recombinations with a code. Be careful with the rapidly increasing number of possible recombinations because it could take long calculation time.
  • Hovering any fragment in the recomposed list will highlight the position in the structure and the coded fragments present in the fragment ion.
  • Clicking in the list will annotate the ion and plot its isotopic distribution in the m/z graph

Experimental data can be pasted and overlaid with the calculated distribution but no similarity scores are given here.

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Do you want to share your results in this page?
The ISIC-EPFL MS team will be delighted to share your updates in ms.epfl.ch! If you want to describe your project using any of our free tools and share your results, you can publish a post describing the project & results and/or once published we could include in our mstoolbox references page. You can also share any of your learning materials contact us. In any case, If you want to be updated, follow us in twitter or linkedln.