Global Proteomics and Proteogenomics

Contact

Maria Pernemalm

ProteomicsCore@scilifelab.se

Recent user publications

The publications in this database are the result of research conducted at the units of SciLifeLab – both in user projects and technology development.

Personnel

Platform Scientific Director:
Prof. Janne Lehtiö, PhD

Head of Unit:
Maria Pernemalm, PhD

Research engineers:
Ghazaleh Assadi, PhD
Xiaofang Cao, PhD
Georgios Mermelekas, PhD
Eduardo Araújo, PhD

Scientists:
Rui Branca, PhD
Rozbeh Jafari, PhD
Henrik Johansson, PhD
Lukas Orre, PhD
Mattias Vesterlund, PhD

Scientific programmer:
Jorrit Boekel, PhD

Bioinformatician:
AnnSofi Sandberg, PhD

Scientific coordinator:
Helena Bäckvall, PhD

Global Proteomics and Proteogenomics

Proteogenomics is a new exciting field in biological mass spectrometry that combines proteomics information with sample specific genomic and transcriptomics information. Applications in proteogenomics include discovery of novel protein coding regions to improve genome annotation; detection of variant and mutated proteins based on DNA and/or RNA sequence data; discovery of cancer neoantigens and evaluation of the impact of genomic changes (e.g. copy number alterations, SNPs, mutations, hyper methylation) on the proteome. We can also provide in-depth proteomics data for comprehensive systems biology studies.

THE FACILITY IS OPEN AND INVITES SPECIALLY PROJECTS RELATED TO COVID-19 FOR FAST-TRACK SERVICE.

Contacts and service requests through: iLAB platform at KI

For instructions on how to register and login to iLab click here

proteomicscore@scilifelab.se

Services

Personalized proteomics
Individual sequence based search database generation for variant analysis at the protein level coupled with in-depth quantitative proteome analysis.

Disease state/Variant proteomics
Database supplemented with all known SNPs and disease causing genetic alterations. (Can be used when sample specific sequence data is not available.)

Unbiased proteogenomics in any species with a sequenced genome
Six frame translation of genome generated database searches for protein coding genome annotation.

XenoProteomics
Database supplemented with peptides from disease causing pathogens.

Meta proteomics
Proteogenomics analysis based on metagenomics database generation

Plasma proteomics
In-depth global MS-based plasma proteomics

If you need support for other type of MS-based projects please visit our regional core unit : Clinical Proteomics Mass Spectrometry (eg, in-depth proteome analysis, quantitative proteomics, IP-MS, etc) or view what other biological MS based services are available via bioms.se

Services during holidays:

The core unit is not engaging/handling any new requests/projects during summer and Christmas holidays:

  • Midsummer – second week of Aug (~7 weeks)
  • Christmas Eve – first week of Jan (~3 weeks)

Equipments

Mass spectrometers

MS timsTOF Pro, Bruker.

MS Orbitrap Exploris 480, Thermo Scientific.

MS Orbitrap HF Q Exactive, Thermo Scientific.

MS Orbitrap Fusion, Thermo Scientific.

MS Orbitrap Q Exactive, Thermo Scientific.

Peptide separation technologies

HiRIEF (High Resolution Isoelectric Focusing)

Liquid Chromatography (nanoUPLC/HPLC/FPLC) Dionex, Agilent

Robots

Ettan Digester (modified Gilson 215), GE Healthcare Life Science

Pi-pet Sampleprep (modified Tecan Xantus), LAT

Mailing address

SciLifeLab
Proteogenomics
Box 1031
171 21 Solna
Sweden

Visiting address

SciLifeLab
Proteogenomics
Tomtebodav 23A
171 65 Solna
Sweden

Last updated: 2023-02-07

Content Responsible: admin(website@scilifelab.se)