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The Protein Tab provides a protein identification centric view. It displays all identified proteins. The total number of proteins is part of the tab title.

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

You can select the protein that you are interested in by clicking on the respective row in the protein table. This will trigger an automatic update of both the peptide table and the spectrum browser. The list of peptides identifying the selected protein will be updated in the peptide table. Additionally, the spectrum which identifies the currently selected peptide is being displayed.

You can sort the table by a column's values through clicking the title of the column. Sorting can be either ascending or descending.

Protein

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, three extra columns will be added to the protein table: protein name, protein accession status and protein sequence coverage. [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 protein table:

Column Description
Protein This is the original protein accession in the file/PRIDE experiment.
Protein Name Protein name downloaded using the mapped protein accession
Coverage Protein sequence coverage calculated using protein sequence downloaded and its peptide identifications.
Threshold PRIDE protein threshold
#Peptides Number of peptides identifying this protein.
#Distinct Peptides Number of distinct peptides identifying this protein.
#PTMs The total number of post translational modifications identified in the protein.
You can right click within the protein table to open a popup menu where you can search the table or choose to copy the content of an individual cell or a number of rows.
You can click on the hyperlinked protein accession in the Mapped Protein Accession column to open the protein's entry in the respective protein database.

Peptide

A summary on the PTMs is displayed on top of the table. It is in the format of [Distinct modified amino acids - total monoisotopic mass difference]

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.
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
You can click on the magnifying glass icon in the #PTM column to view additional details on the PTMs on a specific peptide.

Spectrum Browser

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

Fragmentation Table

A table to compare the fragment ions identified in experiment with the theoretical fragment ions

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

Other titles: