Integrating Proteomics with Online Knowledge Discovery.
PepTracker® aims to provide an integrated environment for tracking, importing, managing and analysing data related to mass spectrometry. Through intuitive and interactive interfaces, PepTracker® aims to offer an enhanced user experience for knowledge discovery.
Keep a record of experimental parameters for future reference and to add further dimensions to later analysis.
Send automated submissions to the mass spectrometry facility.
Receive automated emails, tracking the progress of samples, and gain online access to raw data files as they become available.
Upload quantitative datasets generated by MaxQuant.
Quickly and easily browse through all of the datasets available in PepTracker®.
Visualise & Analyse
Analyse datasets, with various transformations, using a variety of interactive and flexible charts types.
Download charts in either PNG or JPEG format to include in papers and presentations.
Protein Frequency Library
To date, biological science has relied heavily on the manual analysis of experimental datasets to visualise results. However, the combination of fast paced advances in both instrumentation and experimental techniques has resulted in the production of large datasets, for which manual analysis is no longer feasible.
With the advent of high throughput methods for protein identification, huge volumes of data are being created via mass spectra. The volume and complexity of these data make it impossible to analyse them by manual inspection. These data are a major resource that requires new approaches to manage, analyse and store efficiently, for scientists working within the same institution and collaborating institutes. These problems are further
enhanced by the complexity of the data, the non-consensus on data formats and unavailable data standards. Hence scientists are now heavily reliant on computer-based analysis and visualisation techniques for large datasets.
The Lamond Laboratory is one such group requiring new methodologies for the collection, storage, analysis, and visualisation of large datasets from proteomics experiments, with the aim of discovering patterns and trends, which were not previously visible. The PepTracker®
project is an effort to tackle these issues, with the goal of making advances in the overall management of the data sets being produced by researchers and developing web-based visualisation tools that have access to a rich amount of data from past years of experimentation.
These tools will provide insightful analysis through interactions with individual datasets, as well as allow for comparisons of data produced by different researchers, using both similar and different experimental methods and will thereby help to promote new collaborations and to cross-fertilise projects.
Séverine Boulon, Yasmeen Ahmad, Laura Trinkle-Mulcahy, Céline Verheggen, Andy Cobley, Peter Gregor, Edouard Bertrand, Mark Whitehorn, & Angus I. Lamond
Establishing of a Protein Frequency Library and its Application in the Reliable Identification of Specific Protein Interaction Partners Molecular & Cellular Proteomics
Value of Metadata
Detailed annotation allows for customised searches and an extensive set of dimensions for use when attempting to analyse data.
Record. Submit. Track.
allows extensive recording of metadata associated with the experimental procedure used to create samples, as well as data regarding the mass spectrometry process itself.
This metadata can then be used by PepTracker®
to create an electronic sample submission form for the Proteomics Fingerprints Facility at the University of Dundee. When the researcher chooses to, they can have PepTracker send the electronic form, while they submit their labelled samples to the mass spectrometry (MS) facility.
will continuously poll the proteomics server to check when the samples have been run through the mass spectrometer. Once the raw data files begin appearing, PepTracker®
updates the sample status. When all samples have been processed, PepTracker®
will then send an automated email to the researcher to inform them that their raw data files are available for analysis. Researchers can then download the raw data files from PepTracker®
and carry out the standard quantitative analysis using 3rd party software: Mascot and MaxQuant.
Once quantitated data has been obtained from MaxQuant, researchers can choose to upload the results to PepTracker®
for downstream analysis. PepTracker®
provides a number of tools for this analysis, as well as making use of all uploaded datasets to create a target collection of data that is large enough to be used as a baseline for identifying patterns and trends.
Quick and Easy Browsing of Datasets.
provides a set of different views to browse the datasets available in the PepTracker®
These views include customised icons that allow quick recognition of different types of experiments and datasets, as well as smart folders that provide easy access to the most recently uploaded datasets.
A search feature is also available, which filters datasets dynamically based on keywords entered into the search box.
A variety of chart types are provided by PepTracker®
to visualise data. These include:
- Bar Chart
- Column Chart
- Bubble Chart
- Area Chart
- Line Chart
- Plot Chart
- Network Map
Flexible. Intuitive. Interactive.
provides a range of interactive features with the chart visualisations. These interactive features allow intuitive navigation of datasets and provide the ability to understand data more quickly. Through interacting with the data at the protein level, users can drill-down to discover interesting clusters or individual proteins to explore further.
From the user experience of interacting with the data, it is intended that a better feel for the data cam be obtained and hence, researchers can focus their time and efforts on hypothesis that are grounded in experimental evidence.
The types of features available with PepTracker®
- Scrollable and zoomable axis.
- Option to show/hide series.
- Mouse and slider enabled range selection.
- On click context menus.
- Customisable colours.
- Drag and drop, dynamic overlay of protein groups on a dataset.
- Mouse hover tooltips.
- Filter options.
- Output to JPG and PNG formats.
- Fullscreen mode.
Flexible Protein Search.
The protein search facility allows a user to search for any protein in the human proteome, based on either Uniprot Accession number, protein description or gene symbol.
The PepTracker® search finds and presents a list of all datasets that contain the selected protein. The search results also show a protein-peptide alignment map that visually depicts the reliability of the protein identification in the dataset. Each peptide, used for the protein identification, is highlighted on a bar and string representation of the protein, which provides a quick view of the sequence coverage. Colour coding is also used to show the reliability of identifications with each peptide having a different gradient based on its ratio.
Protein Group Annotation.
There is the option to create three different types of protein groups:
- Sub-selection of a dataset.
- User-defined group.
- Globally available group.
These groups can be used in conjunction with the visualisations to show the intersection of the group with the current dataset.
system is currently not available for use out with the Lamond Laboratory. However, we do have plans to provide access to the tools within PepTracker®
for use by the academic community. In order to join our mailing list and receive up-to-date information about developments, please register your interest here: