Theoretical calculations (2024)

Tool 1

Molecular mass calculator

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

MF from monoisotopic mass (I)

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.

• List of spectra​

  On the middle top panel, you can see the list of the imported experimental spectra. Each spectrum has a description if the data are available. You can see the type ofresolution(either high or low resolution), theinstrumentused, theionisationmethod and theanalyser. It is also possible to download the data file and see the meta data associated.

• Entering a monoisotopic mass​

  When loading an experimental spectrum the tool willautomaticallymake a peak picking (centroid) that will be displayed on the spectrum.

  Zooming in the spectrum will progressively add more and more detailed peaks.

  If you are searching the molecular formula of an unknown product you shouldclick on the label corresponding to the monoisotopic experimental mass.

  It is possible to search for many monoisotopic masses at once. SimplySHIFT+ click on other labels in order to have a comma separated list of monoisotopic mass.

Remember that it is possible to search many monoisotopic masses at once

• Molecular formula from monoisotopic mass​

  This tool allows finding possible molecular formula for a specific observed monoisotopic mass. When the elements are part ofH, C, O, N, F, Cl, Br, I, Si, P and Othe monoisotopic mass corresponds to the peak of the isotopic distribution that has the lowest mass.

  However, by mass we don’t observe a monoisotopic mass directly but always𝑚/𝑧m/zof a charged form. The molecule may be charged positively, negatively, multicharged or also modified by the addition of protons or other charged entities.

  This tool will consider the mass of the electron and the number of charge of the molecule.

  Ionizations​

  In order to observe a neutral molecule the mass spectrometer will charge it using different techniques. This may involve adding protons, remove electrons, etc.

  You can also observe charged molecules resulting of the addition of Na⁺, K⁺, etc.

  In order to evaluate all the possibilities you must enter in the ‘ionizations’ field a comma separated list of all the allowed ionizations.

• Syntax

  You may as well specify multiple charges. Here are some examples of allowed patterns:

  • H+ (addition a proton)
  • H+, Na+, K+ (either a proton, sodium cation or potassium cation)
  • H+, (H+)2, (H+)3 (addition of one, two or three protons)
  • (H+)-1, (H+)-2, (H+)-3 (removal of one, two or three protons)
  • It is also allowed to enter range of ionizations like
    • (H+)1-5, adding between one and five protons
    • (H+)-1–5, removing between one and five protons

Accuracy and charge​

You can specify the accuracy in ppm and the charge of the target molecule using the corresponding input box.

Range of atoms and groups​

If some information about the molecule is known, you can specify it in theRange input.

It is possible to specify the range of atoms and groups in a powerful way.

First, you can specify the range of atoms using the synathax :<atom letter><minimum>-<maximum>.

For example, if we know that there are between 0 and 50 carbon atom and between 0 and 100 hydrogen atom, we can type :C0-50 H0-100

You can also use group specification with the same synthax than the atom :<group abbreviation or molecular formula><minimum>-<maximum>.

For instance, if we know that there are between 0 and 2 (CH2CH2) groups, we can write :(CH2CH2)0-2

Moreover, in order to be more intuitive for a chemist, we can also write known abbreviation likeMe,Bu,Boc…

The icon on the top of the panel show the list of the possible groups abbreviations.

You can also specify isotopes, such as[13C]0-10for example.

Filter by degree of unsaturation​

The result can be further filtered by thedegree of unsaturation.

For stable molecules the unsaturation degree is expected to be greater or equal to zero. Moreover, if it is non-radical molecule the unsaturation degree is integer.

Please note that those filters apply on the molecular formula without the ionization.

Relative mass and MF determination​

This view displays normally the mass of the peaks, but it is also possible to display relative mass to a specific peak.

1. Click on a peak to change theMonoisotopic massvalue

• Click on the checkboxRelative mass on the top right.

It is also possible to display possible molecular formulas for the relative mass. Those are calculating using the following criteria:

• allowed atoms are based on theRanges
• only neutral loss are considered
• the charge of the entity loosing this neutral fragment is defined inCharge, by default 1
• you should change the number in the cellShow MFin order to annotate the peaks with the corresponding MF

It is also possible to define the color of the MF annotation depending on the precision. By default, if no MF is found under a precision of 20ppm no MF is displayed.

Results table​

This tool calculates on-the-fly the possible molecular formula based on a monoisotopic mass and possible ionizations.

The resulting table will contain green background lines if this molecular formula exists in PubChem. This is an excellent way to find plausible molecular formula of unknown products.

The results contain various columns:

• the NON-IONIZED molecular formula
• the monoisotopic mass of the NON-IONIZED molecule
• the unsaturation degree
• the ionization
• the observed mass
• the total charge (with ionization)
• the error in mDa
• the absolute value of the error in ppm

On the right of the results table you have the possibility to show the registered Pubchem molecules by clicking on theicon. There is also a way to find more about the Pubchem candidates by clicking on the search icon, this button will redirect you to the Pubchem panel.

Moreover, it is possible tosearch molecular formula that are included in the original molecular formula. To do this, click on theicon. Depending on what was defined in thepreferences for peak labelpanel, this tool will show the possible molecular formula for each peak. You can choose the range of atoms in the molecular formula that you want in the preferences panel.

Pubchem candidates​

Using the buttonPubchem candidatesyou are able to list all the possible molecular formula that yields to the desired monoisotopic mass with the defined precision. The right column will redirect you to the corresponding PubChem web page.

Couple of points to note:

• PubChem does not provide the isotope information in the molecular formula
• PubChem does not provide the different parts of the molecule in the molecular formula
• PubChem is not consistent with the monoisotopic mass they list on their website

Therefore we have recalculated the molecular formula, monoisotopic mass, charge and molecular weight from the provided molfile. This allows us to have very accurate monoisotopic mass that also deals with isotopes.

Please note that for the calculation of the monoisotopic mass we didn’t consider the charge !

NB: only stable isotopes are considered!

Fragment Assignement (Fragments tab)

t is possible to assign mass spectra by ALT + click on a peak mass value. If the value does not appear you need to zoom before on the peak.

In the table you can double-click in theassignment column to enter the corresponding value. Then you will obtain a spectrum with annotations on the top:

Isotopic distribution similarity (Similariy tab)

Searching by monoisotopic allows quickly find possible molecular formula, but there are plenty of information in the isotopic distribution.

The tabSimilaritywill calculate the match between the predicted and experimental isotopic distribution for the specifiedZone.

Peak width will be calculated automatically based on the experimental spectrum and the formula is expected to be good. However, the similarity calculation depends on the mass precision and this parameter has to be setup correctly. If the system cannot calculate correctly the relation between the width and the mass, it is possible to set it manually using the corresponding boxes.

Clicking on one of the result will compare the theoretical versus the experimental isotopic distribution.

Pubchem (Pubchem tab)

This tool allows to find a molecular formula, even if we don’t know the range of atoms that compose the molecule. A few assumptions are made: the charge of the non ionized molecule is null, there are at least 5 molecules that have the same MF and the molecule does not break apart.

When the spectrum is loaded, you can click on a peak and the system will show a list of the possible molecular formula for a given ionization and accuracy. On the table you can see in green the molecular formula that are registered in the PubChem database. If you click on a formula, you can see at the right the list of isomers. In the draw panel, you can make a substructure search or a name search within the list.

In the table you can also see the number ofnatural product(Nat) andbioactive(Bio) molecules with the same molecular formula. If you click on theicon, you can see a table with the publication in PubMed related to the natural or bioactive product. Moreover, usingMeSHterms, you can filtrate the results in the search bar at the top.

The results of the search are displayed in a table. The table includes the structure of the compounds as well as tags such as the number of taxonomies, activities, patents, mass spectra… It also shows if the compounds is a natural product or not.

On theDetail informationpanel, you can find more information about the compound. On the top of the panel, there are the tags associated with the number of mass spectra, number of patents… Below, there is the structure of the compound without stereochemistry, the number on the right indicates the number of stereoisomers found in the database. By clicking on it, you will find all the structures as well as where it comes from.

Pubmed (Medline): In this section, you will find all the publications associated with the compound. By clicking on the title of the publication, you will be redirected to the Pubmed page. The number on the right of each title indicates the number of times that this compounds has been described in the publication. A green color indicates that the publication can be interesting. This allows the user to quickly find the most relevant publications. The three dots next to the number allow the user to see the abstract of the publication. The abstract includes the mesh terms.

Activities: Activities show additional details on the activities of the compound. It includesSuperkingdom,Kingdom,Phylum,Class,Order,Family,Genus,Species.

Taxonomies details: Taxonomies section shows the taxonomy tree of the compound. The depth of the tree can be controlled in the search panel, described above.

Patents: Similar to the Pubmed section, this section shows the patents associated with the compound. By clicking on the title of the patent, you will be redirected to the associated page. Again, the number on the right indicates the number of times that this compounds has been described in the patent. The three dots next to the number allow the user to see the abstract of the patent.

Obviously, all sections can be expanded and collapsed by clicking on the arrow on the right.

The other iconappears when there are experimental spectra from the GNPS database. If you click on this icon, you will be able to compare your spectrum with spectra of molecules that have the same molecular formula from real experiments. You can change experimental spectra using the arrows in you keyboard.

In the table on the top you can see the list of available spectra. For each spectrum, there are information about the ion source, the instrument used to make the measure, the precursor, the ionization, the mode and the export icon redirects you to the original web page where the spectrum comes from. You can also see the similarity between your spectrum and the ones from the GNPS database. Your spectrum as well as the selected experimental spectra are plotted in a head to tail plot.

In the left text entry boxes, you can select the number of peaks that you want to see as well as the accuracy that you allow when comparing with the experimental spectrum from the database. The mass power and intensity power are a way to make either the mass or the intensity more important when comparing with the experimental spectrum. The higher is a power, the more important becomes the information (intensity or mass). The similarity between two spectra is calculated based on thecosine similarity.

On the bottom left panel, you can select any experimental spectrum that was imported.

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.