Peptigram is a web application designed to create visualisations for peptidomics data.

Data processing

Only one input file is required for use, a CSV file, with the minimum data fields as described below. Once uploaded, the input file is processed and the extracted data is stored. Peptigram does not modify the user's data, except where required to correct for the peptide start and end positions relative to the signal peptide.


For each precursor protein in the data set, two types of visualisation are created:

  1. Peptide profile
  2. Peptide alignment map

Peptigram workflow

Input file

The input file consists of a CSV file (other delimiters such as tabulations are also accepted).

Column names authorised

The following column names are required by Peptigram:

Peptide sequence
peptide , sequence
Precursor protein ID
Leading razor protein , UniProt ID , protein
Peptide start
start position , start
Peptide end
end position , end
Samples intensity (multiple samples accepted)
intensity X , sample X , where X is the sample name

Data from MaxQuant/Andromeda

If you use MaxQuant with Andromeda to process your mass spectrometry data, the peptides.txt file from the combined/txt folder can be directly used as input for Peptigram. No modification needed.

Data from other peptide search engine and from de novo peptide sequencing

Currently Peptigram only supports output from MaxQuant/Andromeda. Should the user wish to analyse data from other peptide search engines or from de novo peptide sequencing tools (e.g. X!Tandem, SEQUEST or PEAKS) they will need to format their data file according to the column names outlined above. Peptigram input file requirements are flexible, if there is sufficient demand we may try to accommodate the output of other peptide search engines.

UniProt IDs

Peptigram relies on ProViz to retrieve the precursor protein sequence and associated data. Currently, ProViz only supports UniProt protein data meaning that Peptigram can only accept input with Uniprot IDs.


Download example data

Sequence Protein Start position End position Intensity s1 Intensity s2 Intensity s3
YAKPAAVR P02668 61 68 10217133333.0 0.0 5866233333.0
VVPPFLQPEVMGVSK P02666 98 112 0.0 15626666667.0 690976666.7
YQKFALPQYLK P02663 171 181 16302666667.0 115413333.3 0.0
AASDISLLDAQSAPLR P02754 25 40 101109333.3 677593333.3 15728000000.0
IPAVFKIDALNENKVLVLDTDYKK P02754 78 101 144627333.3 10271766667.0 6429900000.0
TPEVDDEALEKFDKALKALPMHIR P02754 125 148 17024000000.0 0.0 0.0

Summary table

Once the data is uploaded and stored the user is automatically redirected to a summary page. At the top of this page a summary table is found, where each row represents a precursor protein. The table columns include the following information:

  • Name of the precursor protein
  • Description / common name of the protein
  • Organism (linked to the NCBI taxonomy database)
  • UniProt ID of the precursor protein (linked to UniProt)
  • The number of unique peptides from this precursor protein across all samples
  • Maximum peptide ion intensity across all samples for this precursor protein
  • Peptide coverage (%), with a summary diagram of coverage. The grey zones represent regions of the precursor protein containing at least one peptide from at least one sample. White space indicates protein regions where no peptides were detected. Clicking on a grey zone redirects the user to the peptide alignment map for that protein region.

Every column in the summary table can be sorted. By default the table is sorted according to the maximum peptide intensity for the data set. To save space the table spans over multiple pages (if required). A search field is provided to locate specific proteins of interest. The user can navigate to the peptide alignment map of any protein by selecting the associated radio button (to the left) and pressing the Peptide alignment map button.

peptide profile (documentation)
Summary table

Peptide profile

Each sample is represented on a separate line. For each residue (on the x axis), a green bar is drawn if this position is covered by at least one peptide in the given sample. The height of this bar is proportional to the count of peptides overlapping this position. The colour intensity is proportional to the summed ion intensities of peptides overlapping this position, with dark green indicating high peptide intensity and light green indicating low peptide intensity.

The user can select which samples are displayed, as well as choose how to normalize the peptide intensities (either globally or per protein). The count of peptides overlapping a residue and the sum of their intensities is displayed by hovering over the bar. This visualisation can be downloaded as a SVG file.

peptide profile (documentation)
Peptide profile of α-lactalbumin digested by ArgC, LysC and a combination of both peptidases.

Peptide alignment map

The peptide alignment map displays the precursor protein sequence with the detected peptides for each sample mapped to their associated position.

ProViz and precursor protein tracks

ProViz is used to build this visualisation and to retrieve relevant information from public sequence databases (e.g Pfam domains, modifications, known peptides etc.) A multiple sequence alignment for each precursor protein is supplied by a local version of ProViz, meaning at this time only GeneTree alignments containing Uniprot IDs are available.

In the peptide alignment map, separate tracks are included for the peptide profile of each sample, as well as for the alignment, various sequence features and for every peptidase (see below).

Sample tracks with mapped peptides

Each sample from the input data set is represented in a dedicated track. Peptides detected in a sample are displayed in green boxes, where the sequence of the peptide is overlaid. Each box is mapped to the relative position of the peptide within the precursor protein. The colour intensity is proportional to the detected ion intensity of the peptide. More information is available by clicking on a peptide box (see peptide information box).

Cleavage site tracks

Cleavage sites of common endopeptidases can be displayed in separate tracks (per endopeptidase). Each site is represented by a box (2 residues long) which overlaps the cleavage site. The colour of the box is peptidase specific and is consistent across the visualisation. Missed cleavage sites in the users data are represented by translucent boxes. Dashed red lines can be added to track the cleavage site across the entire visualisation (see cleavage site lines).


More information is displayed by hovering over each box. Peptigram is highly interactive and allows the user to select from various options to optimise their visualisation. All interactivity features are explained below.

The PDF button allows the user to download the visualisation as displayed on screen (i.e. with the user selections/modifications if active).

peptide profile (documentation)
Peptide alignemnt map of α-lactalbumin digested by ArgC, LysC and a combination of both peptidases. Visualisation resized to show residues from 1 to 68.


Peptide information box

search sequences

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:

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 peptides

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.

search sequences

Vertical selection of the visualisation

vertical selection

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)
vertical selection interface

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 .

export peptides

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.

export sequences

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.



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.


How to create a new job?

  1. Ensure your input file conforms to the specifications
  2. Go to the new job page
  3. Select your input file
  4. Name your project (optional)
  5. Click on the Submit job button

upload of a new data file

Upload form

How to cite peptigram?

Peptigram is currently developed by Jean Manguy from the Shields lab, UCD Conway Institute of Biomolecular and Biomedical Research; funded by Food for Health Ireland and by the Irish Research Council.

If you use Peptigram please cite the following article.

Peptigram: a web-based application for peptidomics data visualization Jean Manguy, Peter Jehl, Eugene T. Dillon, Norman E. Davey, Denis C. Shields, and Thérèse A. Holton Journal of Proteome Research (2016)
view article online download Bibtex


Find a bug, a typo? Have a feature request? Please create an "issue" on Bitbucket.