Journal of Biotechnology
Journal of Biotechnology
5 years ago

Computational proteomics tools for identification and quality control

Computational proteomics is a constantly growing field to support end users with powerful and reliable tools for performing several computational steps within an analytics workflow for proteomics experiments. Typically, after capturing with a mass spectrometer, the proteins have to be identified and quantified. After certain follow-up analyses, an optional targeted approach is suitable for validating the results. The de.NBI (German network for bioinformatics infrastructure) service center in Dortmund provides several software applications and platforms as services to meet these demands. In this work, we present our tools and services, which is the combination of SearchGUI and PeptideShaker. SearchGUI is a managing tool for several search engines to find peptide spectra matches for one or more complex MS2 measurements. PeptideShaker combines all matches and creates a consensus list of identified proteins providing statistical confidence measures. In a next step, we are planning to release a web service for protein identification containing both tools. This system will be designed for high scalability and distributed computing using solutions like the Docker container system among others. As an additional service, we offer a web service oriented database providing all necessary high-quality and high-resolution data for starting targeted proteomics analyses. The user can easily select proteins of interest, review the according spectra and download both protein sequences and spectral library. All systems are designed to be intuitively and user-friendly operable.

Publisher URL: www.sciencedirect.com/science

DOI: S0168165617314955

You might also like
Discover & Discuss Important Research

Keeping up-to-date with research can feel impossible, with papers being published faster than you'll ever be able to read them. That's where Researcher comes in: we're simplifying discovery and making important discussions happen. With over 19,000 sources, including peer-reviewed journals, preprints, blogs, universities, podcasts and Live events across 10 research areas, you'll never miss what's important to you. It's like social media, but better. Oh, and we should mention - it's free.

  • Download from Google Play
  • Download from App Store
  • Download from AppInChina

Researcher displays publicly available abstracts and doesn’t host any full article content. If the content is open access, we will direct clicks from the abstracts to the publisher website and display the PDF copy on our platform. Clicks to view the full text will be directed to the publisher website, where only users with subscriptions or access through their institution are able to view the full article.