Community Network in MetaProteomics (ComProt)

The aim of the ComProt project is to raise the profile of methods to recover MetaProteomes (MPs) and MetaExoProteomes (MEPs) to increase the opportunity among UK scientists to recover activity data from in situ, real time ecosystem studies which are capable of facilitating the study of complex interactions between components of the community. We will provide advice, workshops and online help tools to highlight effective methods to both extract and analyse MPs and MEPs using existing databases of LC-MS-MS spectral data collected at Warwick SLS by the groups of Elizabeth Wellington and Joseph Christie-Oleza. We are partnering with Jagroop Pandhal at Sheffield where expertise exists in the use of metaproteomics to address problems of algal blooms and provide understanding of the use of MPs in freshwater ecosystems. This will complement the expertise and data on soil community analysis (Wellington) and marine ecosystem expertise and data (Christie-Oleza). We aim to use the data to illustrate different platforms and pipelines to identify proteins both in the total MP and in the MEP. This will be accompanied by the work and expertise of Christopher Quince who has established novel pipelines for metagenomics using assembly-based analysis to recover metagenome assembled genomes (MAGs) which will play an important role in matching spectral data to identify peptides and proteins using translated genes recovered using metagenomes (MGs), and metatranscriptomes (MTs) if available.  Therefore, we can summarise our aims as follows:

  1. Inform UK academic community about ComProt and raise awareness.
  2. Exemplify work flows using data and projects available at Warwick and Sheffield
  3. Disseminate results and pipelines using a workshop held at Sheffield and add an MP stream to ComMet website hosted by Warwick.

Objectives:

To address our research aims we have six objectives which serve as work packages WP1-6:

WP1. Improve the ComMet web site and add details about MPs and MEPs with details about methods and existing publications with statement of aims and objective of ComProt and advertise workshop scheduled for May 2019.

WP2. Use the postdoctoral effort of 7 months (Warwick 5 months and Sheffield 2 months with planned frequent monthly trips for Warwick PDRA to Sheffield) to complete analysis on existing spectral data to encompass the following stages:

  • Methods for preparation of exoproteomes, trypsin in-gel proteolysis and nano-LC-MS/MS analysis
  • Peptide identification through MS/MS database searching
  • Bioinformatic analysis of detected proteins
  • Evaluation of the Galaxy-P platform
  • Development of improved pipelines for protein identification

WP3. Approaches to collection of metagenomes and detailed pipeline approaches to conduct assembly-based MGs and assembly of MAGs.

WP4. Following detailed comparative analysis of MPs and MEPs use ComMet to upload results and provide a review paper to disseminate results and methods as widely as possible.

WP5. Workshop for dissemination of work flows and bioinformatics pipelines for protein identification using MGs as well as integration with associated omics data and traditional ecology datasets. WP6. An open competition to perform metaproteomics on test environmental samples

WP6. An open competition to perform metaproteomics on test environmental samples.