liu.seSearch for publications in DiVA
Change search
ReferencesLink to record
Permanent link

Direct link
A metaproteomics-based method for environmental assessment: A pilot study
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
2013 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

Metaproteomics, as a proteomic approach to analyse environmental samples, is a new and expanding field of research. The field promises new ways of determining the status of the organisms present in a sample, and could provide additional information compared to metagenomics. Being a novel field of research, robust methods and protocols have not yet been established. In this thesis, we examine several methods for a reliable extraction of protein from soil and periphyton samples. The extraction should preferably be fast, compatible with downstream analysis by mass spectrometry and extract proteins in proportion to their presence in the original sample. A variety of methods and buffers were used to extract proteins from soil and periphyton samples. Concentration determinations showed that all of these methods extracted enough protein for further analysis. For purification and digestion of the samples, several methods were used. The purified samples were analysed on three different mass spectrometers, with the Orbitrap Velos Pro delivering the best results. The results were matched against four genomic and metagenomic databases for identification of proteins, of which the UniProt/SwissProt database gave the best result. A maximum of 52 proteins were identified from periphyton samples when searching against UniProt/SwissProt with strict settings, of which the majority were highly conserved proteins. The main limitation for this type of work is currently the lack of proper metagenomic databases.

Place, publisher, year, edition, pages
2013. , 53 p.
Keyword [en]
environmental samples, metaproteomics, liquid chromatography, polyacrylamide gel electrophoresis, mass spectrometry
National Category
Other Chemistry Topics Biochemistry and Molecular Biology
URN: urn:nbn:se:liu:diva-99416ISRN: LiTH-IFM-A-EX-13/2747-SEOAI: diva2:656965
Subject / course
Chemical Biology
2013-09-23, Jordan-Fermi, Fysikhuset plan 4, Linköpings Universitet, Linköping, 10:15 (English)
Available from: 2013-10-18 Created: 2013-10-17 Last updated: 2013-10-21Bibliographically approved

Open Access in DiVA

A metaproteomics-based method for environmental assessment(1619 kB)641 downloads
File information
File name FULLTEXT01.pdfFile size 1619 kBChecksum SHA-512
Type fulltextMimetype application/pdf

Search in DiVA

By author/editor
Fröberg, Henric
By organisation
ChemistryThe Institute of Technology
Other Chemistry TopicsBiochemistry and Molecular Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 641 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Total: 184 hits
ReferencesLink to record
Permanent link

Direct link