Settings

Settings - Compound Search (MS)

The settings dialog is opened using the command "Search -> Settings... ". Use F1 to open this help.

This page describes only a selection of parameters important for 'Compound Search - MS, LC-MS, MSI' mode. This mode is similar to the dereplication mode with the difference that the compounds are generated from an input list of chemical elements (i.e., an input database of compounds is not required). For other parameters, see the page for dereplication mode.

See also the tutorials Tutorial 3: Identification of unknown compounds in LC-MS data and Tutorial 5: Identification of unknown compounds in MSI data.

Settings dialog - compound search (MS).

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Theoretical Spectrum/Spectra

Chemical Elements

Define and select chemical elements from which the compounds are generated.

Buttons:

• "Select All" - select all elements in the list.
• "Clear All" - unselect all elements in the list.
• "Add" - add a new item at the end of the list - a valid chemical element must be entered.
• "Remove" - remove selected items from the list.
• "HCON" - clear the list and set the default chemical elements H, C, O, N, S, and P.

Use a colon to limit a number of occurrences of an element (e.g., S:2 means that two occurrences of sulfur are allowed).

Maximum Number of Combined Elements

Maximum number of combined chemical elements.

Basic Formula Check

Apply Senior's filtering rules. See https://doi.org/10.1186/1471-2105-8-105 for more details.

In 'Compound Search - MS, LC-MS, MSI' mode, the rules are applied to generated compounds. In other modes, the rules are applied to combinations of neutral losses, see https://doi.org/10.1021/acs.analchem.0c00170 for more details.

Advanced Formula Check

Advanced filtering rules are applied if molecular formulas of compounds are generated. See the tables 1, 2, and 3 in https://doi.org/10.1186/1471-2105-8-105 for more details.

N/O Ratio Check

Check if the number of nitrogen atoms is less or equal to the number of oxygen atoms.

Calculate FDRs

Calculate FDRs for LC-MS and MSI data (experimental feature). It can optionally be disabled to cut the processing time in half.

Minimum Intensity of Highest Peak in Isotopic Pattern

Enter the minimum relative/absolute intensity of the most intense peak in an isotopic pattern. Isotopic patterns with relative/absolute intensities below this value will be kept in the spectrum but not annotated.

Isotope m/z Tolerance

The maximum m/z error of difference between an isotopic peak and the most intense peak in an experimental and theoretical isotopic pattern (0 = disabled) [ppm].
Example, let's have two matched peaks in an isotopic pattern of a compound, an isotopic peak with m/z error 7 ppm and the most intense peak with m/z error 4 ppm:
if m/z Error Tolerance = 10 ppm (i.e. <-10,10>), Isotope m/z Tolerance = 0 ppm (i.e. disabled) => the compound is reported as a correct hit;
if m/z Error Tolerance = 10 ppm (i.e. <-10,10>), Isotope m/z Tolerance = 2 ppm (i.e. <0,2>) => the compound is discarded because 7-4=3 is bigger than 2.

Isotope Intensity Tolerance

The maximum error tolerance of intensities of matched isotopes (0% or 100% = disabled) [in % of relative intensity of the most intense peak].
Example:
Isotope Intensity Tolerance = 10%, Relative Intensity of the Most Intense Peak = 100% => the tolerance of relative intensities of isotopes is 10%;
Isotope Intensity Tolerance = 10%, Relative Intensity of the Most Intense Peak = 50% => the tolerance of relative intensities of isotopes is 5%; etc.