Sequence Editor

For some mMass modules and tools like Protein Digest or Peptide Fragmentation it is essential to have a peptide or protein sequence defined. mMass therefore offers a simple internal Sequence Editor [Tools → Sequence Editor] icon. Sequence can be written manually or imported from ASCII, FASTA or mMass documents and any post-translational modification can be set to a single amino acid or to selected type. Some relevant sequence information are shown in the module control panel. There are also three additional tools available for sequence filtering, converting and searching of a sub-sequence by specified mass or by sequence pattern using regular expression syntax.

sequence editor

Sequence editor.

Sequence editing

You can write your sequence manually or import from ASCII, FASTA and mMass documents [Sequence → Import Sequence…] icon. The editor automatically checks validity of your input and does not allow you to write or import any non-amino acid character to sequence window. When the sequence is imported or copied from clipboard some characters are removed without any notice (like whitespaces etc.). If the sequence contains other non-valid characters, these are removed too and shown in a warning dialog. This filtering is especially useful when you copy/paste your sequence from the internet sources where numbers are also included.

Modifications

Any post-translational modification can be set to a single amino acid or to selected type [Sequence → Modifications…] icon. There is currently a list of about 90 pre-defined modifications (according to UNIMOD website); others can be simply defined [Config → Modifications…].

modifications dialog

Modifications dialog.

Sequence Converter

As a part of the Sequence Editor there is a simple Sequence Converter also available [Tools → Sequence Converter…]. Using this converter you can easily convert your sequence from 3-letter to 1-letter representation, filter non-amino acid character or convert a sequence from DNA or RNA to amino acids.

sequence converter dialog

Sequence converter dialog.

Search for Mass

Using the Search for Mass tool [Sequence → Search for Mass…] icon you can search your sequence for any peptide of specified mass. This tool is very useful for identification of the peaks resulting from non-specific cleavage of protein.

search for mass dialog

Search for mass dialog.

Search for Sequence

Using the Search for Sequence tool [Sequence → Search for Sequence…] icon you can search your sequence for any specified pattern. To define a pattern you can write some sub-sequence or regular expression syntax can be used.

search for sequence dialog

Search for sequence dialog.