The following table lists the parameters on the Coverage page of the Protein Identification Details view.
Command or Option | Description |
|---|---|
Description box | Displays the description of the protein. This information is identical to that found in the Description column of the Proteins page. |
Annotate PTMs Reported in Uniprot | Determines whether the application displays the PTMs reported in the UniProt database. Default: Selected This parameter is not available if no annotation information is available. |
Show Only PTMs | Determines whether the application displays all modifications classified as artifacts, chemical derivatives, isotopic labels, and synthetic peptide protection groups. Default: Cleared |
Include PSMs That Are Filtered Out | Determines whether the application displays PSMs that it found but had filtered out via display filters. Default: Cleared |
Coverage | (Read-only) Displays the percent coverage calculated by dividing the number of amino acids in all found peptides by the total number of amino acids in the entire protein sequence. |
Found Modifications | (Read-only) Lists all identified PTMs. The list is the same as the list on the Modification List page. Each modification is listed with a single-letter abbreviation, its name, and target amino acids. |
Uniprot PTMs | Lists the type of PTMs found in UniProt for the protein. |
PTM Site Probabilities | Displays an estimate of the likelihood, in percentages, that phosphorylation will occur on an amino acid, if site localization scores are available from the ptmRS node. For information on how ptmRS calculates these scores, see IMP-ptmRS node. |
Threshold | Displays categories of probability that a modification will occur on a sequence site. For example, when you choose 25 from the Threshold list, the Protein Identification Details view displays modifications that have a low (25–100%) probability of occurrence on a site. |
Sequence page | |
Protein sequence coverage bar | Represents the protein sequence. The colored areas represent portions of the protein sequence that have been matched by peptides. The protein sequence coverage bar is colored to indicate the confidence of the peptide sequence identification as follows:
The numbers on top of the protein sequence coverage bar indicate how many amino acids the protein sequence contains, in increments of 100, and correspond to the numbers in the column to the left of the sequence table. |
Sequence table | Displays the complete amino acid sequence of the currently selected protein file, including PTMs. The application highlights (in a color that represents its confidence in the identification) portions of the sequence that match the searched sequence. The numbers in the column to the left of the sequence table and the numbers in the header on top of the sequence table are intended to orient you when you want to find automatically assigned amino acid numbers in the table. The application displays numbers in the left column in increments of 100, and they correspond to the numbers on top of the protein sequence coverage bar. The numbers on top of the table are displayed in increments of 10. In the 11-20 column, the first row displays the 11th to 20th amino acid, the second row displays the 111th to 120th amino acid, and so on. For more information on the sequence table, see Sequence Page. |
Modification List page | |
Position | Displays the position of the amino acid in the protein sequence. |
Target | Displays the one-letter code for the modified amino acid. |
Modification | Displays the name of the PTM. |
Classification | Displays the classification of the PTM according to UniProt database. |
Highest PTM Score | Displays the most likely PTM site as calculated by the algorithm associated with the ptmRS node. The application displays this column only if site localization scores are available. |
Sequence Motif | Displays the biologically significant amino-acid sequence pattern surrounding the site of the PTM. A lowercase character indicates a modified amino acid. |
Highest Peptide Confidence | Displays the highest peptide confidence that the modification is reported in. |
Number of Amino Acids Displayed Before and After the Modification | Specifies the number of amino acids that appear before and after the PTM in the Sequence Motif column. Minimum: 0; maximum: 100 Default: 6 |