Settings

Settings - Direct Comparison of Experimental and Theoretical Spectrum (MS/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 'Compare Peaklist(s) with Spectrum of Searched Sequence - MS/MS' mode. For other parameters, see the page for dereplication and de novo sequencing modes.

See also the tutorials Tutorial 6: How to compare a theoretical spectrum with a peaklist ?, Tutorial 6: Annotate MS/MS spectrum of a metabolite, and Tutorial 9: Draw Peptide Tool.

Settings dialog - direct comparison of experimental and theoretical spectrum (MS/MS).

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Searched Sequence/Compound

Sequence

A peptide sequence which you are searching for or a peptide sequence tag. A peptide sequence must be entered if "Mode" is set up to "Compare Peaklist(s) with Spectrum of Searched Sequence". Otherwise, the option is similar to "Peptide Sequence Tag" with a difference that a peptide sequence candidate is not removed from the search but it is just highlighted in the output list of peptide sequence candidates. If "Compare Peaklist(s) with Spectrum of Searched Sequence" mode is used, the only possible format of the expression is a peptide sequence (e.g.,

[Val]-[Lac]-[Val]-[Hiv]-[Val]-[Lac]-[Val]-[Hiv]-[Val]-[Lac]-[Val]-[Hiv]

or

[Pro]-[Ile]-[Ile]\([Orn]-[N-Ac-Ile]\)[Phe]

). Regular expressions like

([Val]-[Lac]-[Val]-[Hiv]-*){3}

are not supported in this mode. See also Format of Sequence Databases.

N-terminal Modification

A name of an N-terminal modification which belongs to the searched peptide. The name must be defined in N-/C-terminal Modifications File.

C-terminal Modification

A name of a C-terminal modification which belongs to the searched peptide. The name must be defined in N-/C-terminal Modifications File.

Branch Modification

A name of an N-terminal or C-terminal modification which belongs to a branch of a searched peptide (branched and branch-cyclic peptides only). The name must be defined in N-/C-terminal Modifications File.

Formula

If 'Peptide Type' is set to 'Other', we can define a formula of a neutral molecule instead of a 'Sequence'. This feature is useful for fragmentation of secondary metabolites with structures which cannot be represented as sequences of building blocks. See the Tutorial 6: Annotate MS/MS spectrum of a metabolite.