Protein View report

The protein view of an entry on the hit list can be displayed by clicking on an accession number in a summary report.

Sequence information

Information about the protein, the enzyme (if any), and any modifications are printed at the top of the page. This is followed by the formatted sequence of the protein in 1-letter code with matched peptides highlighted in bold, red type.

If the sequence database was nucleic acid, and the matches all came from a single frame, the report will be very similar to that for a protein database entry. If the matches come from multiple frames, because of a frame shift or splice, then only one frame at a time will be displayed. A drop down list can be used to switch between frames.

Peptide match table

The sequence block is followed by a detailed table of the peptide matches. For an enzyme digest, you can also choose to display all the calculated peptides, whether matched or not, including all partials up to the limit specified by the Missed Cleavages parameter. The matched peptides are shown in bold, red type, together with a link to the corresponding peptide view. If no enzyme or a semi-specific enzyme was used, this option is not available, and the table contains only the matched peptides.

If the enzyme was a mixture of independent enzymes, and you choose to display calculated peptides, these will be shown for one enzyme component at a time. A drop down list can be used to switch between enzymes. The formatted protein sequence shows highlights for all matches at all times.

The default sort order is start residue order. Controls are provided to re-display the table sorted by increasing or decreasing peptide molecular weight

Precursor mass error graph

A graph displays the mass differences between the calculated and experimental mass values for the protein match in the same units as were used to specify the peptide mass error tolerance. There is also a figure for the RMS error of the set of matched mass values in ppm.

Sequence annotations

If available, at the bottom of the page, the full text of the sequence annotations is reproduced. The text is downloaded from a public server such as UniProt or NCBI. If Mascot Server is behind a firewall or proxy server, you may need to allow access to these resources in the firewall or proxy server.

Genomic sequences

If the match is to a very long nucleic acid sequence, (greater than 30,000 bases by default), the conventional Protein View is impractical. In this case, Mascot will automatically generate a DDBJ/EMBL/GenBank format feature table. For example:

BLASTCDS        422..469
               /label=Q103
               /colour=2
               /note=”Mascot match, … sequence=GLGTDEDTLIEILASR”
               /blastp_file=”../data/20001016/FTGrCfc.dat”
               /mass=1701.88
               /score=82
               /rank=1
               /translation=”GLGTDEDTLIEILASR”
BLASTCDS        603..650
               /label=Q105
               /colour=2
               /note=”Mascot match, … sequence=SEDFGVNEDLGDSDAR”
               /blastp_file=”../data/20001016/FTGrCfc.dat”
               /mass=1738.73
               /score=82
               /rank=2
               /translation=”SEDFGVNEDLGDSDAR”

By default, only matches with significant scores (p < 0.05) are output. A different score threshold can be specified by appending &_featuretableminscore=X to the protein view URL, where X is the score threshold.

The feature table can be saved to a text file and read into a genome browser such as Artemis from the Sanger Centre. This provides a very flexible and powerful way to view Mascot peptide matches in genomic sequence data.

URL switches for protein_view.pl