Proteins View Page¶
The protein view page provides a table view of crosslinks or looplinks at the protein level. Each row in the table corresponds to a unique crosslink ( specific position in protein A linked to a specific position in protein B) or a unique looplink (specific pair of positions in a protein). The data may be filtered according to confidence, taxonomy, or individually by protein. For the view page seen when merging multiple searches, see Merged Protein View Page.
Note: If any identified peptides map to multiple proteins, those proteins are listed here as separate rows. For example if peptide 1 is linked to peptide 2, and peptide 1 maps to protein A and peptide 2 maps to proteins B and C, rows will be present for A-B and A-C. This may dramatically increase the number of reported crosslinks if your protein database is redundant in terms of homologous proteins or proteoforms or if small peptides are mapping to many proteins. The filtering options described below are meant to help eliminate this redundancy in reported proteins.
General Options¶
Change Searches¶
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:
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¶
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¶
Project owners may click “Save as Default” to save the current URL as the default view of the “Protein 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.
View Looplinks¶
By default, the table shows crosslinks. To switch to looplinks, click the [View Looplinks] link at the top of the table. To view crosslinks again, click the [View Crosslinks] link that appears at the top of the table.
Download Data¶
All crosslinks and looplinks that meet the current filtering criteria may be downloaded as tab-delimited text by cliking the [Download Data (#)] link above the table. # indicates the number of rows in the table.
Download UDRs¶
UDR stands for “unique distance restraint”, which takes its name from 3D modelling terminology. A UDR, in proxl, is any specific position in a protein linked to a specific position in another protein, whether it is a crosslink or a looplink. The [Download UDRs (#)] link downloads a non-redundant tab-delimited text table of these UDRs consolidated from the crosslinks and looplinks. The # is the number of UDRs.
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 more information about the search, including the path the data were imported from, the linker that was used, the upload date, and the FASTA file that was searched.
Filter Data¶
The data presented may be filtered according to the following criteria. Note: Only crosslinks or looplinks that meet ALL the filter criteria are shown.
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”:
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.
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.
Peptide Filters¶
Some search algorithms, such as Percolator, provide statistics at the peptide level that may be used for filtering. If applicable, peptide-level filtering options may be set here. 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”:
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.
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.
Exclude links with¶
Crosslinks or looplinks that have any of the checked attributes will be excluded. The attributes are:
- no unique peptides - If all peptides that ID either one of the crosslinked proteins also map to another protein
- only one PSM - If a given crosslink or looplink was identified by a single PSM
- only one peptide - If a given crosslink or looplink was identifed by a single peptide, where a peptide is the combination of sequence, linked positions, and modifications
Exclude organisms¶
Any links containing a protein that maps to any of the checked organisms will be excluded. The list of organisms presented was gathered by the proteins found in the search. Useful for filtering out groups of contaminant proteins.
Exclude protein(s)¶
Any links containing a any of the selected proteins will be excluded. Multiple proteins may be selected or unselected using control-click (command-click on the mac) or shift-click. Useful for filtering out individual contaminant proteins.
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 “Protein View” for this search.
Table Description¶
Above the table is the text “Crosslinks (#)” or “Looplinks (#)”. # is the number of rows in the table. The [View Looplinks (#)] links will change to viewing looplinks, where # is the number of looplinks that will be shown. The [Download Data (#)] link downloads the data as tab delimited text (see Download UDRs) and [Download UDRs (#)] downloads the UDRs as tab delimited text (see Download Data).
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.
Protein 1 and 2 (Crosslink-only)¶
In the case of crosslinks, these are the crosslinked proteins
Position (Crosslink-only)¶
This is the crosslinked position in the respective proteins, where the first residue is counted as position 1.
Protein (Looplink-only)¶
In the case of looplinks, this is the looplinked protein
Position 1 and 2 (Looplink-only)¶
In looplinked proteins, these are the positions in the protein that are linked.
PSMs¶
The total number of PSMs (peptide spectrum matches) meeting the cutoff that identified either crosslinked (crosslink view) or looplinked (looplink view) peptides that mapped to the reported proteins and positions.
# Peptides¶
The total number of identified crosslinked (crosslink view) or looplinked (looplink view) peptides that mapped to the reported proteins and positions. Only peptides that meet the current filtering criteria are counted.
Note: The individual peptides may be viewed by clicking a row in the table to view a table of peptides. Rows in that peptide table may also be viewed to view the underlying PSMs and view spectra. See View Peptides.
# Unique Peptides¶
Of the # of peptides, the total number that uniquely mapped to this protein pair (crosslink view) or protein (looplink view).
Best Peptide-level Scores¶
If peptide-level filters are being used, the best score from all peptides matching to the indicated proteins and positions will be displayed for each filter.
Best PSM-level Scores¶
If PSM-level filters are being used, the best score from all PSMs matching to the indicated proteins and positions will be displayed for each filter.
View Peptides¶
All peptides that meet the current filters that were mapped to a protein-level crosslink or looplink may be seen by clicking on the respective row in the table. Additionally, all rows of this peptide table may clicked to view all PSMs associated with that peptide identification. (See View PSMs.)
Columns¶
The peptides appear in a table with the following columns:
Reported peptide¶
The peptide identificaton as it was reported by the respective search program.
Peptide 1 and 2 (Crosslink-only)¶
The sequences of the two crosslinked peptides.
Pos (Crosslink-only)¶
The positions in the respective peptides that were crosslinked (starting at 1).
Peptide (Looplink-only)¶
The sequence of the looplinked peptide.
Pos 1 and 2 (Looplink-only)¶
The positions in the peptide that were looplinked.
Scores¶
A column for each peptide-level score is shown.
# PSMs¶
The number of PSMs that meet the cutoff criteria that identified this peptide.
Best PSM-level Scores¶
If PSM-level filters are being used, the best score from all PSMs matching to this peptide for each score on which PSMs are being filtered.
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.
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.
Scores¶
A column for each PSM-level score or annotation.
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 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.