In-house Tools for Advanced MS Data Analysis

You will find here different tools for advanced mass analysis of high resolution mass spectra. Various tools, accessible from the menu, will help you to analyze complex mass spectra and solve specific problems.

Among the various tools:

1. Calculation

Calculate your theoretical spectrum

The User can draw or copy a structure (as smiles or mol files), or directly write the elemental composition of the molecule. The resolution can be chosen. The molecule has to be charged to be observed in MS, so the ion species has to be given. Multiple ion species can be calculated, separated by a comma. Click on “predict mass spectrum”. The user can paste from clipboard / drop a mass spectra, select the experimental spectra in the list to overlay with the theoretical.

Find a Molecular Formula from a monoisotopic mass (MM)

From an experimental mass, an ion species, a given molecular formula range of elements and for a given mass precision, this tool allows to find possible molecular formula by testing all possible combination of atoms. The result is a list of molecular formula, with mass errors. The theoretical mass spectrum can be displayed by selecting the MF (green) and superimposed with another one by scrolling in the list (red). Among the possible MFs, PubChem candidates matching the monoisotopic mass can be listed with the structure.

MS/MS fragment calculation

This tool allows the User to generate fragments from a drawn or pasted molecule as a smiles or molfile. The modifications (ion species) expected have to be added. Select the blue circle and click on the bonds to cleave it. The list of possible fragments are listed, and the list of possible molecules with expected experimental masses.

2. Similarity to spectrum

Drag&Drop your experimental spectrum and identify your molecular formula

The User first paste the experimental mass spectrum in the “superimpose experimental spectrum Box”. The User can selected ranges of expected elements and groups of elements with ranges min-max.  The User should add the expected charges (like H+, (+), Na+…).  In the option, resolution parameters should be adjusted (Width top and bottom of peaks), together with the comparison zone around the monoisotopic mass (which depends on the isotopic pattern complexity). Process. The list of matched ions of the experimental spectrum is displayed with the similarity score and global charge. The overlay between experimental and theoretical is automatically displayed in the bottom window when selecting a line.

Extend your search using all elements

This tool allows to find possible molecular formula based on a molecular formula range. Any element can be specified from the “Atom range selector” table. In order to assist in the selection of the elements, the following information are displayed for each element:

  • Nb iso: the number of isotopes
  • iso 5%: number of isotopes with over 5% abundance
  • % Δ-3: relative abundance of the isotope at a distance of -3Da compare to the more abundant isotope
  • % Δ-2: relative abundance of the isotope at a distance of -2Da compare to the more abundant isotope
  • % Δ-1: relative abundance of the isotope at a distance of -1Da compare to the more abundant isotope
  • % Δ1: relative abundance of the isotope at a distance of 1Da compare to the more abundant isotope
  • % Δ2: relative abundance of the isotope at a distance of 2Da compare to the more abundant isotope
  • % Δ3: relative abundance of the isotope at a distance of 3Da compare to the more abundant isotope

The element selector based on isotopic abundance of each isotope can be used to select possible elements. The User should define the minimal and maximal number of each atom in the proposed molecular formula, and chose if this element should be present only once or not.

The measured monoisotopic mass should be given, as well as classical parameters of modifications, peak width, and zone of comparison (Low and High) around the monoisotopic peak.

3. Peptides

Predict CID/ETD spectra from a sequence

This tool allows to calculate a, b, c, x,y,z and immonium fragments from a peptidic sequence, copied / pasted directly as a one letter or 3 letters code (sequences can be copied directly from UniProt or Pdb). One protonated, the 1 letter code sequence is displayed as 3 letter codes and any modification can be added after each residue written ().  Example HAlaLysGlyProHisLeuSer(Ph)ThrOH for a Phenyl group on S.

Apm2s: Match your experimental data

This tool allows to identify in complex mass spectra possible adducts of a protein/peptide, but also ions generated by enzymatic digestion and MS/MS fragmentation. The idea is to combine all possible molecular formula and test the similarity based on an experimental spectrum. A complete User Guide is provided and an example can be loaded.

4. EasyCont

This tool allows to identify possible known contaminants in the pasted experimental mass spectrum based on a list of defined database of contaminants listed in a Google spreadsheet. The ionization type and mode can be selected. Typical parameters such as comparison zone and peak width (top and bottom) have to be defined. The User can use his own Google spreadsheet library by selecting “Custom” , adding it in the list and selecting it before the processing.

Contact Luc Patiny for any question, help or request on ChemInfo.