Analysis of Protein Sequencing Data Types

Protein sequencing generally refers to the determination of the amino acid sequence of a protein. This involves ordering the amino acids in the protein to determine their exact order within the protein. The data results of protein sequencing can be described as the following types of data.

 

Amino Acid Sequence

This is the main output of protein sequencing, expressed as a string composed of the single-letter codes of 20 standard amino acids. For example, a small protein fragment may have the sequence "MGSDKI".

 

Mass Spectrum Data

If mass spectrometry is used for protein sequencing, a mass spectrum will be obtained, displaying different mass-to-charge ratios and relative intensities. This can help determine the mass and composition of amino acid fragments.

 

Coverage Map or Mapping

This shows how the protein fragments with determined sequences are mapped back to the whole protein. This can help researchers understand how much of the protein sequence has been determined and which areas are still undetermined.

 

Confidence Scores

For each determined amino acid position, there may be a confidence score indicating the degree of confidence in the identification of the amino acid at that position.

 

Other Annotations

These may include known post-translational modifications, subunit information, known structural domains, etc.

 

Typically, amino acid sequence data can be stored in simple text formats, such as the FASTA format. Mass spectrum data, on the other hand, is usually saved in specialized formats, such as .mzML, .mzXML, or .raw format.