The Proteomics application makes Protein and peptide analysis intuitive, simple and accessible by combining the four essential programs of needed for analysis in one single tool.
The goal is to create a tool that combines all the different applications needed for protein and peptide analysis. We develop a workflow application that allows users to analyse and compare proteins and peptides in one instead of four programs.
Until now biologist at Unilab Basel had to juggle multiple tools if protein and peptide samples from muscle tissue needed to be analyse. Presently samples collected by the hospital, or your physician end up being run through the different programs and subsequently analysed in lab by the biologists. Done so by using multiple independent applications. Transferring data automatically between tools is currently not possible. Also remains valuable data, from the public domain momentarily inaccessible to researchers with the limited computational recourses available.
M.Ataman, Biozentrum Basel
The «dockerised»* Proteomics workflow application being developed combines the four main applications. Biologists can run the search and analysis on a single application by choosing the peptide or protein of interest and select the desired workflow. MsFragger, Philosopher, Ion-Quant and Nextflow run in the background simultaneously before the data survey is displayed. It allows users to discover novel proteins that used to be measured but overlooked in the public available mass spectrum data. This will not only facilitate the linking, reuse and build up of knowledge in molecular biology, it will also provide access to the momentarily inaccessible data. *programming term for containerised
The Proteomics application allows users to discover novel proteins that used to be measured but overlooked in the public available mass spectrum data. This will not only facilitate the linking, reuse and build up of knowledge in molecular biology, it will also provide access to the momentarily inaccessible data.
The project duration is two semesters (Ip3/4).Our team comprised seven members in IP3. In the second semester of the project, our team comprised six members with one further member leaving the team midway.
University of Basel
Klingelbergstrasse 50/70
Basel, BS 4056
Website: biozentrum.unibas.ch
| Prename | Name | Role IP3 semester | Role IP4 semester | |
| Sean | Blackburn | sean.blackburn@students.fhnw.ch | DEV | PO |
| Sebastian | Hugentobler | sebastian.hugentobler@students.fhnw.ch | DEV | SM |
| Robin | Delimar | robin.delimar@students.fhnw.ch | DEV | DEV |
| Simon | Freiermuth | simon.freiermuth@students.fhnw.ch | SM | DEV |
| Claire | Smits | claire.smits@students.fhnw.ch | DEV | DEV |
| Lea | Burki | lea.burki@students.fhnw.ch | PO | P2P/PO |
Bernhard Wyss
