Sequence Editor
Use the internal Sequence Editor to define a protein or peptide sequence to be available for digestion or fragmentation. Using the standard sequence editor any sequence can be manually typed, pasted from clipboard or imported from any mMass or FASTA document.
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Custom-Type Sequence Editor
Using the custom-type sequence editor, any non-standard peptide sequence consisting of up to 20 monomers can be created. You can choose monomers from build-in library consisting of more than 500 items or you can define your own. Type monomers manually into corresponding fields or use drag and drop from Monomer Library panel.
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Sequence Modifications
Apply and post-translational modification to a single amino acid or selected type. In addition, you can specify whether it should be fixed or variable for all possible variants to be calculated in related tools. In order to avoid permanent assignment of the same modification set, define your own presets and use it frequently.
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Protein Digestion
Many experiments, involving, protein validation, modification detection etc., apply a specific enzymatic digestion of a protein with known sequence. Protein Digest tool provides a tool to generate a list of peptides resulting from in-silico digestion of your protein sequence. You can easily compare this list of theoretical peptides with acquired data too see any matches.
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Peptide Fragmentation
Different types of fragmentation techniques can be used for peptide sequence validation, as well as for the detection, localization and characterization of modifications. For these types of experiments, common fragments of a peptide sequence can be generated in-silico using the Peptide Fragmentation tool.
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On-Line Protein Identification
One of the most common task in proteomics is protein identification. mMass provides a unified interface for the three major protein identification tools available on-line. You can easily send acquired data directly to Mascot, ProFound or Protein Prospector tools and see the results in your web browser.
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H/D Exchange Fitting
For the hydrogen/deuterium exchange experiments it is essential to determine incorporation of deuterium into a peptide molecule. In general, Envelope Fit tool calculates all the possible isotopic patterns for specified formula and exchanged atom and uses their linear combination to fit modeled patterns to acquired data. Percentage of each individual state as well as average incorporation are shown as a result.
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