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 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. |
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 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 |
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.