Welcome to the user manual of Protter - a webservice and webapplication to visualize the sequence, topology and annotations of individual proteins.
You can access the interactive webclient at https://wlab.ethz.ch/protter to create protein plots.
Alternatively you can programmatically use the webservice at https://wlab.ethz.ch/protter/create using a set of defined parameters.
You can also download a pdf-version of this user manual here.
If you have additional questions, encounter any error or bug, or have suggestions on how to improve Protter, please contribute to the Protter Discussion Group.
More documentation on:
This is how the web interface looks like: In the upper region, there are four tabs to specify various settings. While in the lower region, there is the actual protein visualization. Whenever you change a parameter, the visualization will automatically refresh and show your changes instantaneously.
Typically, you will go through the following steps as indicated at the top of the screen:You start at the "protein" settings where you specify the protein that you want to visualize. Just enter the UniProt protein identifier of your protein. You can also provide gene names and Protter will ask you back in case that this gene name is ambiguous within UniProt.
In case you want to visualize an arbitrary amino acid sequence, simply switch to "by sequence" and enter your sequence in the textbox:
Specification of the protein's sequence has generated a first visualization using default parameters. In the "topology" settings, you can fine tune the protein's topology.
A protein's transmembrane topology consists of: N-terminus location, transmembrane regions and, optional, membrane anchors:
In the first panel, you can switch between "no membrane", "automatic" (default) and "custom".
In Protter, Styles are used to highlight certain regions of the protein sequence by varying four parameters:
The "styles" settings shows a table of all currently specified styles. Each row represents a style and has 8 columns:
If highlighted regions (partly) overlap, styles defined further down will override styles defined further up. You can drag-and-drop the rows in the table using the double-arrow on the very beginning of each row to reorder the priority of your styles.
Click at the end of the style table to add a new empty style.
Click at the end of the style table to remove all styles at once.
In the "misc." settings you can modify details of the protein visualization.
On top of visualizing your protein of interest you can also load a list of proteins, browse through the visualizations, and download a combined visualization of all proteins as one PDF document or as ZIP archive of separate files. This is particularly useful to visualize results of mass-spectrometry based proteomics studies.
"TPP ProtXLS" — First, in the ProteinProphet web-interface, filter the list of proteins as desired (e.g. by probability). Then export the results as Excel file: Download the exported file to your disk (example file).
"TPP PepXLS" — First, in the PeptideProphet web-interface, filter the list of peptides as desired (e.g. by probability). Then export the results as Excel file: Download the exported file to your disk (example file).
"Mascot" — First, in the Mascot web-interface, select "export as CSV": Then you can filter the peptides and proteins (e.g. by ionscore) and export to a CSV file. Download the exported file to your disk (example file).
"MaxQuant" — Locate the "evidence.txt" file of your MaxQuant analysis and optionally prefilter it (e.g. by PEP) using e.g. Microsoft Excel.
"Skyline" — After installing the Protter Skyline plug-in (download), you will find a Protter report under File > Export > Report...: Select Protter and click Export to generate a suitable .csv file.
By clicking a protein, Protter will immediately load the selected protein in the visualization pane. Additionally, if specified, the list of peptides of this protein will be shown.
Clicking a peptide sequence will select (see Visualization section) the corresponding region on the amino acid sequence in the protein visualization:
Click reset to unload all proteins/peptides and reset Protter to start over again.
Click export all... to open up the export all proteins dialog:
Note: the public Protter server is currently limited to 100 proteins in batch export. To generate visualizations of bigger protein lists you can download and setup your own local Protter server. See Installation & Requirements of the Server software section below.
All parameters have to be separated by a &
e.g.: create?param1¶m2¶m3&...
To specify a sequence you can either enter the sequence itself via the seq parameter
e.g.: seq=ELVISISALIVE
or a Uniprot Name or Accession by the up parameter.
e.g.: up=CD44_HUMAN
Note: only one of both should be set.
tm is used to set the transmembrane regions. This parameter is optional and will result in a visualization without a membrane if omitted.
e.g.: tm=phobius.tm
Note: if tm=auto transmembrane topology will be automatically determined, which is equivalent to nterm=UP.NTERM&tm=UP.TRANSMEM&anchor=UP.LIPID for a UniProt identifier
and nterm=PHOBIUS.NTERM&tm=PHOBIUS.TM for any other given sequence.
nterm specifies the location of the protein's N-terminus. It can be intra | extra | up.nterm | phobius.nterm.
This parameter is optional and will result in a visualization without a membrane if omitted.
e.g.: nterm=intra
anchor specifies regions of membrane anchors which will be considered in the visualisation of the protein's topology.
e.g.: anchor=UP.LIPID
specifies the requested image format. Currently supported formats are svg | png | pdf.
e.g.: format=svg
mc sets the membrane color.
e.g.: mc=lightsalmon
lc sets the transmembrane label color.
e.g.: lc=blue
tml sets the transmembrane label style and can be either none | numcount | alphacount | Alphacount | romancount | Romancount.
e.g.: tml=Alphacount
Note: the value is case sensitive!
specifies the positions where potential enzymatic cleavage should be indicated. This parameter is usually used with a peptidecutter-region.
e.g.: cutAt=peptidecutter.Tryps
override the default labels at the membrane (intra & extra).
e.g.: lblin=Nuclear&lblout=Perinuclear%20space
add this parameter to get number-labels at every 10th residue.
e.g.: numbers
Note: this parameter does not need a value.
adds a centered title to the top of the protein plot.
e.g.: title=MyProtein
add this parameter to include a legend of all defined styles right next to the protein plot
e.g.: legend
Note: this parameter does not need a value.
A style is defined and applied to a collection of regions as a single parameter:
e.g.: style=regionA[,regionB,...]
Numerous styles may be displayed by treating them as individual parameters (i.e. separated by a &).
A style is made up of one or more comma separated style-parameters: p1:v1[,p2:v2,...]
Later style definitions will override previous ones and if a style-parameter is omitted the value of the previous style will be used.
Following style-parameters are available:
Regions are a collection of one or more individual regions. The individual regions are to be separated by commas.
e.g.: regionA[,regionB,...]
An individual region can be either:
When specifying a Phobius region, the protein sequence will be sent to a Phobius server for topology prediction. The URL of the Phobius server can be set in the configuration file. Following Phobius prediction annotations are supported:
PHOBIUS.TM
: transmembrane regionsPHOBIUS.C
: cytoplasmic loopPHOBIUS.NC
: non cytoplasmic loopPHOBIUS.SP
: signal peptideUniprot provides numerous annotations for its proteins. See http://www.uniprot.org/manual/sequence_annotation for all available Uniprot sequence annotations including descriptions and examples.
PeptideCutter provides a webservice to in-silico digest protein sequences. PeptideCutter regions will refer to the amino acids immediately preceding the reported cleavage sites.
Regular Expressions are a mighty concept for defining protein sequence motifs. To build regular expressions with live feedback http://www.gethifi.com/tools/regex provides a helpful tool.
Note: The protter web application may be called using the same parameters as the ProtterServer:
https://wlab.ethz.ch/protter/#param1¶m2¶m3&...
This urls allow interactive editing of the pre-coded visualization and can be readily bookmarked or send via email.
The ProtterServer is a webservice to visualize the sequence, topology and annotations of individual proteins. The server is written in Java. The webserver functionality is based on NanoHTTPD (version 1.21). For visualization a request is transformed into a TeX file which is processed within a LaTeX distribution (e.g. MiKTeX) by the TeXtopo package. Textopo takes care of the layout of protein topology. The resulting dvi file is converted to a svg file using dvisvgm. The initial svg is further processed to include the specified styles. Optionally, the resulting svg may be converted to a png or pdf image using the Apache Batik toolkit. To allow for visualization of annotations ProtterServer is using several other webservices to resolve sequence specific protein annotations. Currently UniProt, Phobius and PeptideCutter can provide sequences and annotations.
The Protter web application is a browser based interactive client for the Protter server. It is based on the AJAX framework jQuery (version 1.9, http://jquery.com/) extended by following plugins:
Protter not only displays your custom protein annotation but also retrieves and displays computed/curated annotations from various sources:
Various parameters require the specification of a color. You can choose from 140 SVG compatible colors (see below) or specify any color by a hexadecimal code (e.g. FF0000
for red).
aliceblue | antiquewhite | aqua | aquamarine | azure | beige |
bisque | black | blanchedalmond | blue | blueviolet | brown |
burlywood | cadetblue | chartreuse | chocolate | coral | cornflowerblue |
cornsilk | crimson | cyan | darkblue | darkcyan | darkgoldenrod |
darkgray | darkgreen | darkgrey | darkkhaki | darkmagenta | darkolivegreen |
darkorange | darkorchid | darkred | darksalmon | darkseagreen | darkslateblue |
darkslategray | darkslategrey | darkturquoise | darkviolet | deeppink | deepskyblue |
dimgray | dimgrey | dodgerblue | firebrick | floralwhite | forestgreen |
fuchsia | gainsboro | ghostwhite | gold | goldenrod | gray |
green | greenyellow | grey | honeydew | hotpink | indianred |
indigo | ivory | khaki | lavender | lavenderblush | lawngreen |
lemonchiffon | lightblue | lightcoral | lightcyan | lightgoldenrodyellow | lightgray |
lightgreen | lightgrey | lightpink | lightsalmon | lightseagreen | lightskyblue |
lightslategray | lightslategrey | lightsteelblue | lightyellow | lime | limegreen |
linen | magenta | maroon | mediumaquamarine | mediumblue | mediumorchid |
mediumpurple | mediumseagreen | mediumslateblue | mediumspringgreen | mediumturquoise | mediumvioletred |
midnightblue | mintcream | mistyrose | moccasin | navajowhite | navy |
oldlace | olive | olivedrab | orange | orangered | orchid |
palegoldenrod | palegreen | paleturquoise | palevioletred | papayawhip | peachpuff |
peru | pink | plum | powderblue | purple | red |
rosybrown | royalblue | saddlebrown | salmon | sandybrown | seagreen |
seashell | sienna | silver | skyblue | slateblue | slategray |
slategrey | snow | springgreen | steelblue | tan | teal |
thistle | tomato | turquoise | violet | wheat | white |
whitesmoke | yellow | yellowgreen |