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Peptides View Page

/images/peptide-page.png

The peptide view page provides a table view of the data at the peptide level. That is, all peptides (and crosslinked peptide pairs) identified by the search software may be viewed on this page--along with accompanying peptide spectrum matches (PSMs) and tandem mass spectra. The data presented may be filtered according to confidence, type of peptide, and which modifications are present on the peptide. Note, this document covers the peptide view page for a single search. For the view page seen when merging multiple searches, see :doc:`/using/merged-peptide`.

Search Information

The name of the search (and internal search ID reference number) from which these data were obtained is shown first. The red [+] icon may be clicked to reveal details about the search.

Search Details

The "Path" is the location on disk from which the data were imported. The "Linker" is the name of the crossinker used in the experiment. "Search Program(s)" is the name and version number of the PSM search software used. "Upload date" is the date the data were uploaded into proxl. "FASTA file" is the name of the FASTA file used to perform the PSM search.

General Options

Change Searches

/images/peptide-page-change-searches-link.png

The "Change searches" link allows the user to change which searches are currently being displayed. Clicking the link causes the following overlay to be displayed:

/images/change-searches-overlay.png

Select or de-select searches by clicking on them in the list. Once done, click "Change" to update the page with the new data or "Cancel" to close the overlay.

Update From Database

/images/peptide-page-button-update.png

If the user changes any filter parameters--such as PSM/peptide score cutoffs--this button must be clicked to reflect the new filter choices.

Save as Default

/images/peptide-page-button-save-as-default.png

Project owners may click "Save as Default" to save the current URL as the default view of the "Peptide View" for this search. This default view will be populated with the same options as when the button is clicked. This is a convenient way to share data with collaborators or the public that does not require that they manipulate the image viewer to see the data.

Share Page

/images/peptide-page-button-share-page.png

Clicking the "Share Page" button will generate a shortcut URL for viewing the current page. The shortened URL will appear in an overlay as:

/images/share-page-overlay.png

Copying and sharing the highlighted URL will direct users to the view of the page when the URL was generated. Note that this URL does not grant access to the page to any user that would not otherwise have access.

Filter Data

The data presented may be filtered according to the following criteria. Note: Only peptides that meet ALL of the specified criteria are returned.

PSM Filters

The filters to apply at the PSM level. Only results which have at least one PSM that meets all of the selected critiera will be listed. When listing PSMs associated with peptides, only PSMs that meet all of the selected critiera will be listed.

To change the PSM-level filters, first click the pencil icon next to "PSM Filters":

/images/filter-change-psm-filter1.png

This opens an overlay with the containing the possible score types to use as PSM filters for this search. To change the cutoff values to be used for any of these score types, enter the value next to the score type. proxl will correctly handle scores for which larger values are more significant or scores for which smaller values are more signiciant.

/images/filter-change-psm-filter2.png

To save the new values to the page, click the "Save" button. To cancel, click "Cancel".

The "Reset to Defaults" button will reset the cutoff values to the defaults specified by the proxl XML file uploaded to the database. This typically represents the suggested cutoffs by the author of the respective search program.

Important: It is necessary to update the data on the page after changing filter cutoff values. After clicking the "Save" button, you must click the "Update" button on the page to apply any new PSM- or peptide-level filters.

/images/filter-update-from-database.png

Peptide Filters

The filters to apply at the peptide level. Only results which have at least one peptide that meets all of the selected critiera will be listed.

To change the peptide-level filters, first click the pencil icon next to "Peptide Filters":

/images/filter-change-peptide-filter1.png

This opens an overlay with the containing the possible score types to use as peptide-level filters for this search. To change the cutoff values to be used for any of these score types, enter the value next to the score type. proxl will correctly handle scores for which larger values are more significant or scores for which smaller values are more signiciant.

/images/filter-change-peptide-filter2.png

To save the new values to the page, click the "Save" button. To cancel, click "Cancel".

The "Reset to Defaults" button will reset the cutoff values to the defaults specified by the proxl XML file uploaded to the database. This typically represents the suggested cutoffs by the author of the respective search program.

Important: It is necessary to update the data on the page after changing filter cutoff values. After clicking the "Save" button, you must click the "Update" button on the page to apply any new PSM- or peptide-level filters.

/images/filter-update-from-database.png

Type filter

Only peptides of the checked type(s) will be returned. Proxl defines the types as:

  • crosslink - A pair of peptides linked by a crosslinker.
  • looplink - A single peptide with two residues linked by a crosslinker.
  • unlinked - The peptide without a crosslinker on any residue.

Checking multiple boxes will include any peptide that has at least one of the checked types. I.e., checking 'crosslinks' and 'looplinks' will only include peptides that are either crosslinks or looplinks. Only checking 'crosslinks' will only return crosslinked peptides.

Modification filter

Only peptides with at least one of the checked modifications will be included. Note that monolinks are considered modifications of residues in proxl, so the mass of the crosslinker when found on monolinks is included here.

Update

In order to apply new filter parameters to the shown data, the "Update" button must be clicked. This will fetch filtered data from the proxl server and display the data on the web page.

Save As Default

Project owners may save the current filter parameters as the default view of the data on this page by clicking this button. This default view will be shown when users follow links to the "Peptide View" for this search.

Table Description

Above the table is the text, "Peptides (#)", where # is the number of distinct reported peptides were found for this search. A distinct peptide is the combination of peptide sequence(s), linked positions in those peptides, and the location and type of post-translational modifications.

Columns

The columns are described below. Note that all column headers may be clicked to toggle between ascending and descending sorting of that column. Holding the shift key while clicking column headers allow sorting on multiple columns.

Type

The type of peptide (crosslink, looplink, or unlinked).

Reported peptide

The peptide as it was reported by the search program used.

Peptide 1

The parsed sequence of the peptide (or the first peptide in the case of crosslinks).

Pos

The position in that peptide containing the linker.

Peptide 2

The parse sequence of the second peptide in the crosslink.

Pos

The position in that peptide containing the linker.

Protein 1

The protein(s) to which the first peptide matches, and the position in that protein to which the linker position in that peptide matched. Mouse-over the protein name to get a description.

Protein 2

The protein(s) to which the second peptide matches, and the position in that protein to which the linker position in that peptide matched. Mouse-over the protein name to get a description.

Peptide-level Scores

If peptide-level scores are available for this search, the scores will appear as separate columns.

Best PSM-level Scores

Columns will appear for each PSM-level score on which the results are currently being filtered. Each of these columns will show the best PSM-level score for each respective PSM-level filters. E.g., if p-value is being used as a PSM-level score, the best PSM p-value will be displayed for each peptide.

View PSMs

All PSMs meeting the current filtering criteria that map to a given peptide can by shown by clicking on the table row containing that peptide.

/images/peptide-page-view-psms.png

Columns

The PSMs appear in a table with the following columns:

Scan Num.

The scan number from the spectral file (e.g., mzML file)

Charge

The predicted charge state of the precursor ion.

Obs. m/z

The observed m/z of the precursor ion.

RT (min)

The retention time in minutes.

Scan Filename

The filename of the scan file.

PSM-level scores

Each PSM-level score will appear as a separate column.

View Spectra

The annotated mass spectrum may be viewed for any PSM by clicking the "View Spectrum" link. For help on our spectrum viewer, see the :doc:`/using/spectrum-viewer` page.

Sort Data

All column headers may be clicked to toggle between ascending and descending sorting of that column. Holding the shift key while clicking column headers allow sorting on multiple columns.

Download Data

Clicking the [Download Data] link will download the shown data as a tab-delimited text file.