Documentation

Peptide information box

The "peptide information box" is displayed when you click on any peptide box of interest. On the left of this panel, there are options to copy the peptide sequence, highlight a vertical section of the visualisation relating to the peptide, and buttons to query the peptide in the following external tools:

• The peptide database PeptideAtlas
• The peptide database PepBank
• The bioactivity prediction tool PeptideRanker

On the right, a table summarises the intensities of the selected peptide in every sample. Here, the selected peptide is highlighted in blue. When a peptide is not present in a sample (as defined by the dataset) the intensity cell is left blank.

Search peptides

You can search for a specific peptide or multiple peptides using regular expressions via the Search peptides button. When the use regular expression switch is off only the exact input peptide will be matched (if present). Peptides not matching the query are obscured to highlight the matched peptides. The reset button — next to the Search peptides button — resets the visualisation.

Search sequences

You can search for motifs in the precursor protein (and alignment where available) using regular expressions via the Search sequences button. The matching residues will be highlighted in bold. The search is carried out on the actual sequence, meaning you don't need to account for indels ( - ). The reset button — next to the Search peptides button — resets the visualisation.

Vertical selection of the visualisation

In order to focus on particular part of the visualisation, sub regions can be selected in a number of ways. The selected region remains visible, while the rest is obscured. This can be useful for interpretation when you have multiple samples and multiple data tracks. The different ways to select a vertical region are as follows:

• Use the slider above the precursor protein sequence and then click on the Focus button
• Directly input the residue positions of interest and then click on the Focus button
• Hold the ctrl key and click on a data box (e.g. a peptide box, a Pfam domain)

Resize the visualisation

If a user is only interested in a particular region of a protein the entire visualisation can be resized accordingly. First, select a section — as described above — and then click on the Resize button. This will redirect you to a new page, where a peptide alignment map of only this sub region is displayed (with the default parameters).

Extract peptides

From the whole precursor protein or from a selected part of the protein you can extract peptides from all or a subset of samples. Click on the Export button and select Export peptides. From here you can directly copy the list of peptides, download a text file containing these peptides or query them in PeptideRanker .

Extract sequences

From the whole precursor protein or from a selected part of the protein you can extract part of the protein sequence or alignment (if available). Click on the Export button and select Export sequences . You can directly copy the sequences or download them as a text file. Sequences can be extracted as is or in fasta format.

Settings and filters

The Settings and filters panel — available from the button of the same name — allows the user to modify the peptide alignment map. Here, the user can alter settings and filter peptides by intensity. Once the user has made their selections the visualisation will be updated accordingly by clicking on Apply.

Protein viewer

If an alignment is available for your data, you may disable it should you wish to. All additional data tracks supplied by ProViz can be hidden also.

Peptides and peptidases

Peptigram displays a peptide track for each sample in the users data. The user has the option to choose which samples to display and which to hide. This can be repeatedly modified and updated as the user requires. The colour intensity of the peptide boxes is relative to the peptide intensity. By default the colour gradient is based on the intensity of only peptides detected for that protein (across all samples). From the normalization list you can select to scale the gradient across all peptides in the entire data set.

By default only the Trypsin peptidase track is displayed. Other peptidase tracks can be added by selecting them from a drop down list. Cleavage sites that don't match the N- or C-termini of detected peptides are represented by translucent boxes. These can be removed via the display missed cleavage sites switch.

Filters

Intensity

Detected peptides can be filtered according to their intensity. To do this the user inputs the minimum and maximum intensities of their choice or selects them via the slider buttons. To implement their selection the user must then click on the Apply button. Peptides outside the selected threshold will be hidden and only peptides within the selected intensity range will be visible. Additionally, the user can select to display the x most or least abundant peptides in their data by either inputting the value or using the dedicated slider. Selections are applied by clicking on the update button.

Cleavage site lines

Cleavage sites can be highlighted across the entire visualisation by clicking on peptidase boxes of interest. Individual lines can be removed by clicking on the peptidase box a second time. The hide cleavage lines button can be used to remove all the selected cleavage site lines.

Overview box

Precursor proteins can be quite large, and often are too long to visualise in their entirety on a computer screen. To account for this, the overview box allows you to quickly move along the protein sequence (section by section) using the slider button. Equally, the ← and → buttons can be used to navigate along the visualisation (the ← and → keys can also be used). The dashed outline represents the part of the protein currently displayed on screen. When a section of the precursor protein is selected (see Vertical selection of the visualisation), t this is highlighted in grey in the overview box. If the visualisation is resized, the removed sections are represented by the blue stripped boxes.