version 1.0  |  help  |  manual  |  Wollscheid Lab


Welcome to Protter — the open-source tool for visualization of proteoforms and interactive integration of annotated and predicted sequence features together with experimental proteomic evidence!

N-Glyco SRMAtlas
Signal Peptide
N-X-S/T Motif sequence
(regular expression)
Isoform Sequence Variant
Protein Epitope Signature Tag
Phosphorylation Site
Peptide Identification user-uploaded proteomics file
Ambiguous Peptide PeptideClassifier


2018-11-01 new
The in silico human surfaceome website is online now! Explore a new public biomedical resource complementing the Cell Surface Protein Atlas (CSPA) and use it to uncover cellular phenotypes and new surfaceome markers.
#Surfaceome #HumanProteome #CellAtlas
2018-10-31 new
We just published a manuscript on "The in silico human surfaceome" employing a machine learning approach (SURFY). This new public biomedical resource can be used to uncover cellular phenotypes and new surfaceome markers!
#Surfaceome #HumanProteome #CellAtlas #PNAS
2018-10-10 new
Our review/perspective on "Surfaceome Nanoscale Organization and Extracellular Interaction Networks" in "Current Opinion in Chemical Biology" is now online! Here's a share link for free access for 50 days: review
Thanks to editors Ileana Cristea & @lilley_ks!
2018-06-04 new
Protter was cited more than 300 times! It’s great to see how you used Protter in so many ways to visualize your proteoforms! Google scholar
2018-03-15 new
More than 2500 monthly users of Protter! Thank you for using Protter!
Shortened URL links can now be generated for easier sharing of protein visualizations! Try the new 'share' button next to your protein.
Protter now supports UniProt isoform entries (e.g: Q13740-2, CD166-2_HUMAN)! As UniProt's annotation on isoforms is very limited, by default Phobius will be used for topology prediction of protein isoforms.
Added support for Protein XML files as used in the TPP or exported from ProteomeDiscoverer.
Protter's application note in Bioinformatics was one of the journal's top-ten highest cited articles published last year! A big thanks to all the users!
Set up a Google Discussion Group dedicated to Protter.
Custom TeXtopo commands for visualization fine-tuning can be specified via the '4) misc.' tab.
User defined intra-membrane regions can be visualized via the '2) topology' tab.
Added support for direct export to PowerPoint: click the export button and select pptx format!
Protter's Skyline plugin is now available at the new Skyline Tool Store.


The ability to integrate and visualize experimental proteomic evidence in the context of rich protein feature annotations represents an unmet need of the proteomics community. Here we present Protter, a web-based tool that supports interactive protein data analysis and hypothesis generation by visualizing both annotated sequence features and experimental proteomic data in the context of protein topology. Protter supports numerous proteomic file formats and automatically integrates a variety of reference protein annotation sources, which can be readily extended via modular plug-ins. A built-in export function produces publication-quality customized protein illustrations, also for large datasets. Visualizations of surfaceome datasets show the specific utility of Protter for the integrated visual analysis of membrane proteins and peptide selection for targeted proteomics.



In silico human surfaceome new
An interactive tool for exploring the complete list of predicted surfaceome proteins. Allows to visualize and compare surfaceome landscape grouped into their functional classes.
Cell Surface Protein Atlas
A Mass Spectrometric-Derived Cell Surface Protein Atlas based on in depth analysis of 41 human cell types and 31 mouse cell types.

Protter is also linked from a number of tools and databases: To generate the topological layout, Protter internally uses the TeXtopo package.

tips & tricks

Run Protter on your own computer:
You can run Protter on your own server or even on your laptop! Just follow the installation instructions on the Protter download page.
Embed or link Protter images in your own web pages or reports:
Use Protter to create your protein visualization, export it to 'png' format, copy and paste the URL of the png file to your web page or report. Also, have a look at all the parameters encoded in the URL which allows you to generate custom Protter images automatically! More info: linking to Protter.


how to cite

An application note describing Protter has been published in Bioinformatics.
If you use Protter for your research please cite:

Protter: interactive protein feature visualization and integration with experimental proteomic data.
Omasits U, Ahrens CH, Müller S, Wollscheid B.
Bioinformatics. 2014 Mar 15;30(6):884-6. doi: 10.1093/bioinformatics/btt607.

open source

Protter is written in Java and Javascript and is completely open source. The code can be found at GitHub.


Extensive documentation can be found at the Protter help pages.
You can also download a pdf-version of the help document.

linking to Protter

If you want to link to the Protter webinterface, you generate the link using the # sign (here the format parameter is irrelevant as you will end up with the Protter UI in all cases), e.g:
Here you can specify the identifier alone without the additional parameters (they will be set to default values depending on the type of protein).

If you want to directly link to the Protter visualization, you take the same link but replace # with create?, e.g:
Here you have to specify the visualization style using the parameters (here tm=auto) as there are no defaults. And you can specify the file format (here format=png)!

A tip to create the URLs: load a protein in the Protter webinterface and style the topology and visualization settings as needed. Then click the "export" button, select the format and have a look at the URL of the downloaded file. This is a good base to start for automating links to Protter visualizations by customizing the URL.

Check the help page for more details.

frequently asked questions

How to highlight a peptide in my protein?
Select the peptide by clicking at it's first and then on it's last amino acid. Then switch to the "styles" tab and add a new style by clicking at the plus-icon at the bottom of the table. Apply the new style to the selected peptide by clicking at the plus-icon in the region-textbox and selecting the very first entry ("selected range").
How to embed a protein visualization in a PowerPoint slide?
Click on the "export" button on the top-left of your visualization, select the PNG option, and save the resulting image-file to your computer. Open an empty PowerPoint slide, select "Insert > Pictures" and choose the image.
Can I also visualize non-membrane proteins?
Yes, just enter your protein ID or sequence as usual and then switch to the "2. topology" tab and select "no membrane".
Can Protter visualize my Skyline peptides?
Yes, install the Protter plugin from the Skyline Tools Store. Then, in Skyline, select Tools > Protter.
Can I adjust details in the visualization manually?
Yes, click the "export" button next to the visualization and select one of the vector graphic formats (svg or pdf). Save the exported file to your computer and edit it using Inkscape or Adobe Illustrator
Can I create Protter visualizations also programmatically?
Yes, the Protter server provides a RESTful web API for easy access from any scripting language. Check the help page for more details.
Can Protter brew me a cup of coffee or maybe some tea?
No, unfortunately not. But we are working hard on this...
Have more questions? Please post to the Protter Discussion Group or send an email to

applications in the literature

Figure 3 – Genome-wide investigation and expression analysis of Sodium/Calcium exchanger gene family in rice and Arabidopsis.
Singh AK et al. Rice (N Y). 2015 Jul 2.

Figure 2F – Kin of IRRE-like Protein 2 Is a Phosphorylated Glycoprotein That Regulates Basal Insulin Secretion.
Yesildag B et al. J Biol Chem. 2015 Oct 23.

Figure 4E – Evolutionarily conserved intercalated disc protein Tmem65 regulates cardiac conduction and connexin 43 function.
Sharma P et al. Nat Commun. 2015 Sep 25.

Figure S1 – Optogenetic manipulation of cGMP in cells and animals by the tightly light-regulated guanylyl-cyclase opsin CyclOp.
Gao S et al. Nat Commun. 2015 Sep 8.

Figure 3B – The identification of an integral membrane, cytochrome c urate oxidase completes the catalytic repertoire of a therapeutic enzyme.
Doniselli N et al. Sci Rep. 2015 Sep 8.

Figure S6 – Requirement of Fra proteins for communication channels between cells in the filamentous nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120.
Omairi-Nasser A et al. PNAS. 2015 Aug 11.

Figure 1 – Connexin 43 is an emerging therapeutic target in ischemia/reperfusion injury, cardioprotection and neuroprotection.
Schulz R et al. Pharmacol Ther. 2015 Jun 11.

Figure 2 – Proton-dependent glutamine uptake by aphid bacteriocyte amino acid transporter ApGLNT1.
Price DR et al. Biochim Biophys Acta. 2015 May 29.

Figure 4 – Two Proteins Form a Heteromeric Bacterial Self-Recognition Complex in Which Variable Subdomains Determine Allele-Restricted Binding.
Cardarelli L et al. MBio. 2015 Jun 9.

Figure 4B – A chimeric vacuolar Na(+)/H(+) antiporter gene evolved by DNA family shuffling confers increased salt tolerance in yeast.
Wu G et al. J Biotechnol. 2015 Jun 10.

Figure S3 – Homozygous haplotype deficiency reveals deleterious mutations compromising reproductive and rearing success in cattle.
Pausch H et al. BMC Genomics. 2015 Apr 18.

Figure S1 – A Low-Affinity K+ Transporter AlHKT2;1 from Recretohalophyte Aeluropus lagopoides Confers Salt Tolerance in Yeast.
Sanadhya P et al. Mol Biotechnol. 2015 Jun.

Figure 3A – A transient receptor potential ion channel in Chlamydomonas shares key features with sensory transduction-associated TRP channels in mammals.
Arias-Darraz L et al. Plant Cell. 2015 Jan 16.

Figure S1 – An electrostatic interaction between BlpC and BlpH dictates pheromone specificity in the control of bacteriocin production and immunity in Streptococcus pneumoniae.
Pinchas MD et al. J Bacteriol. 2015 Jan 26.

Figure 4 – Experimental Evolution of Species Recognition.
Rogers DW et al. Curr Biol. 2015 Jun 29.

Figure 4 – Pathogenesis, Epidemiology, Diagnosis and Clinical Aspects of Smith-Lemli-Opitz Syndrome.
Bianconi SE et al. Expert Opin Orphan Drugs. 2015 Mar.

Figure 2 – Legionella pneumophila utilizes a single-player disulfide-bond oxidoreductase system to manage disulfide bond formation and isomerization.
Kpadeh ZZ et al. Mol Microbiol. 2015 Jan 30.

Figure 4 – Complete Genome and Phylogeny of Puumala Hantavirus Isolates Circulating in France.
Castel G et al. Viruses. 2015 Oct 22.

Figure 3B – Facilitating the Validation of Novel Protein Biomarkers for Dementia: An Optimal Workflow for the Development of Sandwich Immunoassays.
del Campo M et al. Front Neurol. 2015 Sep 29.

Figure 3 – Diversity of the Epsilonproteobacteria Dsb (disulfide bond) systems.
Bocian-Ostrzycka KM et al. Front Microbiol. 2015 Jun 9.

Figure 4a – Structure-function analysis of CCL28 in the development of post-viral asthma.
Thomas MA et al. J Biol Chem. 2015 Jan 2.

Figure S4 – Mitochondrial genomes of the Baltic clam Macoma balthica (Bivalvia: Tellinidae): setting the stage for studying mito-nuclear incompatibilities.
Saunier A et al. BMC Evol Biol. 2014 Dec 21.

Figure 6a,b – Membrane topology of hedgehog acyltransferase.
Matevossian A et al. J Biol Chem. 2014 Dec 8.

Figure 1b – Shewanella oneidensis cytochrome c maturation component CcmI is essential for heme attachment at the non-canonical motif of nitrite reductase NrfA.
Fu H et al. Mol Microbiol. 2014 Nov 17.

Figure 3b – An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.
Bock T et al. Nucleic Acids Res. 2014 Nov 14.

Figure 6 – ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing.
Pritchard JR et al. PLoS Genet. 2014 Nov 6.

Figure 6 – Screening the Expression of ABCB6 in Erythrocytes Reveals an Unexpectedly High Frequency of Lan Mutations in Healthy Individuals.
Koszarska M et al. PLoS One. 2014 Oct 31.

Figure 2 – Antennal-Expressed Ammonium Transporters in the Malaria Vector Mosquito Anopheles gambiae.
Pitts RJ et al. PLoS One. 2014 Oct 31.

Figure 1 – The connexin43 mimetic peptide Gap19 inhibits hemichannels without altering gap junctional communication in astrocytes.
Abudara V et al. Front Cell Neurosci. 2014 Oct 21.

Figure 7b – Evidence for requirement of CydX in function but not assembly of the cytochrome bd oxidase in Shewanella oneidensis.
Chen H et al. Biochim Biophys Acta. 2014 Oct 11.

Figure 1 and Figure 3 – Pharmacological consequences of the coexpression of BK channel α and auxiliary β subunits.
Torres YP et al. Front Physiol. 2014 Oct 10.

Figure 4 – FRET-Assisted Determination of CLN3 Membrane Topology.
Ratajczak E et al. PLoS One. 2014 Jul 22.

Figure 6 – Identification of Key Residues and Regions Important for Porcupine-mediated Wnt Acylation.
Rios-Esteves J et al. J Biol Chem. 2014 Jun 13.

Figure 2b – N-Glycoprotein Surfaceomes of Four Developmentally Distinct Mouse Cell Types.
Kropp EM et al. Proteomics Clin Appl. 2014 Jun 11.

Figure 1 – A Human Pluripotent Stem Cell Surface N-Glycoproteome Resource Reveals Markers, Extracellular Epitopes, and Drug Targets.
Boheler KR et al. Stem Cell Reports. 2014 Jun 6.

Figure 6 – Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data.
Qeli E et al. J Proteomics. 2014 May 27.

Figure 2 – CCK(-like) and receptors: Structure and phylogeny in a comparative perspective.
Yu N, Smagghe G. Gen Comp Endocrinol. 2014 May 16.

Figure 9 – N-glycosylation and topology of the human SLC26 family of anion transport membrane proteins.
Li J et al. Am J Physiol Cell Physiol. 2014 May 15.

Figure 2 – Subunit CydX of Escherichia coli cytochrome bd ubiquinol oxidase is essential for assembly and stability of the di-heme active site.
Hoeser J et al. FEBS Lett. 2014 May 2.

Figure S5 – Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness.
Liu Y et al. Mol Cell Proteomics. 2014 Apr 22.

Graphical Abstract – Combine and Conquer: Surfactants, Solvents, and Chaotropes for Robust Mass Spectrometry Based Analyses of Membrane Proteins.
Waas M et al. Anal Chem. 2014 Feb 4.

Figure 4 – Proteomic Analysis Reveals Drug Accessible Cell Surface N-Glycoproteins of Primary and Established Glioblastoma Cell Lines.
Bock T et al. J Proteome Res. 2012 Oct 5.

animated demo of Protter

Ulrich Omasits – protter@