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The Peptide Tab provides a peptide centric view. All identified peptides are displayed in this area. The total number of peptides is part of the tab title.

From top to bottom, you can see three main areas of information:

You can select the peptide you are interested in by clicking on the respective row in the peptide table. This will trigger an automatic update of both the PTM table and the spectrum browser. The of PTMs in the selected peptide will be updated in the PTM table. Additionally, the spectrum identifying the selected peptide will be displayed.

You can sort the table according to the column by clicking on the column's title. Sorting can be either ascending or descending.

Peptide

An mass spec experiment often don't contain protein names and protein sequences, these are the key information to interpret the protein identification results. In the PRIDE Inspector, you can click on Update Protein Details to retrieve the complete protein names, protein accession status, protein sequence and protein sequence coverage. Once clicked, two extra columns will be added to the protein table: protein name and fit. [Note that, this requires an active Internet connection]

More information on Obtain Protein Details

You can click on Show/Hide Icon to show or hide columns, and the table below gives a short description for every column in the peptide table:
Column Description
Peptide Sequence The complete peptide sequence is shown with modified amino acids highlighted in red. If you mouse over the peptide sequence, a tooltip with PTM details will be displayed.
Fit whether the peptide sequence fits the protein sequence, it could be unknown when the protein sequence is no available, or fit if the peptide sequence can be found at the given start and stop position of the protein sequence, or fuzzy fit if the peptide position no longer fit, but the peptide sequence can still be found in the protein sequence.
Protein The peptide's protein accession
Modification Post translational modifications on this peptide.
#PSM A number of peptide-spectrum matches
Length Peptide length
pI Theoretical isoelectric point calculated using peptide sequence. See details from here.

PSM

You can click on Show/Hide Icon to show or hide columns, and the table below gives a short description for every column in the PTM table:

Column Description
Peptide Sequence The complete peptide sequence is shown with modified amino acids highlighted in red. If you mouse over the peptide sequence, a tooltip with PTM details will be displayed.
Fit whether the peptide sequence fits the protein sequence, it could be unknown when the protein sequence is no available, or fit if the peptide sequence can be found at the given start and stop position of the protein sequence, or fuzzy fit if the peptide position no longer fit, but the peptide sequence can still be found in the protein sequence.
Ranking The ranking given by the search engine
Delta m/z The difference between the observed and theoretical m/z.
Charge Precursor ion charge
Precursor m/z Precursor ion m/z value.
Modifications A distinct list of PTM accessions with their count
Peptide Score Peptide b1Score given by the search engine, the number of columns depends on the search engine used. For instance, mascot b1Score will be displayed if Mascot search engine is used. Both X correlation and Delta Cn will be displayed for SEQUEST search engine.
Length Peptide length
Start The start position of the peptide within protein sequence.
Stop The stop position of the peptide within protein sequence.
Spectrum Id Spectrum ID

Spectrum Browser

Displays the spectrum identifying the selected peptide.
For more details, please refer to: Spectrum Browser.

Protein Sequence Viewer

The Protein Sequence Viewer can be used to visualize downloaded protein sequence, and colour code it with peptide and ptm identifications.
For more details, please refer to: Protein Sequence Viewer.

See Also