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genform (version 8)

MS data:

MS/MS data (optional):

Structural formula existence check:

Allow only molecular formulas for that at least one structural formula exists or specify advanced restictions, note that the default of genform is 'no existence check'

Experimental molecular mass:

(default: mass of MS basepeak)

Type of ion measured:

Accuracy of measurement of MS1:

In parts per million

MS match value:

Select output type of the MS match value

Allowed deviation for full acceptance:

of MS/MS peak in ppm

Allowed deviation for total rejection:

of MS/MS peak in ppm

Threshold for the MS match value:

Threshold for the MS/MS match value:

Threshold for the combined match value:

Sort generated formulas by:

Chemical element filtering:

Formulas must have at least one hetero atom:

Apply Heuerding-Clerc filter:

Weighting of m/z for MS/MS match value:

Intensity weighting for MS/MS match value:

Allow odd electron ions for explaining MS/MS peaks:

Excess of double bond equivalent for ions:

Output options for main outputs

Output options for main output 0

Additional output data sets

Additional output data sets 0

Overview

Genform generates candidate molecular formulas from high-resolution MS data. It calculates match values (MV) that show how well candidate molecular formulas fit the MS isotope peak distributions (MS MV) and the high-resolution MS/MS fragment peak masses (MSMS MV). Finally it computes a combined match value from these two scores. This software can be regarded as a further development of the ElCoCo and MolForm modules of MOLGEN-MS with a clear specialization towards MS/MS.

Input

MS and MS/MS centroided spectra are given as tab separated files with two columns:

m/z
intensity

Output

Main output containing a list of all possible molecular formulas, further options can be chosen:

if the explained peaks shall also be written to the output
if the explanation shall be given as molecular formulas for the fragment or as neutral losses
double bond equivalents for each molecular formula
calculated ion masses
output match values in percent

Output structure:

molecular fomula / (double bond equivalent) / (calculated mass) / ppm / MS MV / MSMS MV / combined MV

ppm: The value ppm denotes the relative deviation of the calculated mass of the molecular ion from the mass of the basepeak (basemass) in the MS in parts per million (ppm).

MS MV: It is calculated from measured and theoretical isotope peak intensities. The MV ranges from 0 to 1. The better theoretical and measured isotope distributions fit, the higher is the MV. There are three different algorithms implemented for calculating the MS MV, which are nomalized dot product, nomalized sum of squared errors and the normalized sum of absolute errors.

MSMS MV: It shows how well the masses of the MS/MS fit possible fragments of the candidate molecular formula. Again, the MS/MS MV is a value between 0 and 1, whereby higher values reflect a better fit.

combined MV: combined match value

Example output:

C4H9N3O2

132.07675

-0.8

96.674

100.000

96.674

Advanced options

For undersanding of the parameters and rules for creating possible molecular formulas, see the manual of the commandline tool for info.