Global Proteomics and Proteogenomics


Maria Pernemalm

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.


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
Konstantin Barylyuk, PhD
Mahnaz Nikpour, PhD

Rui Branca, PhD
Rozbeh Jafari, PhD
Henrik Johansson, PhD
Lukas Orre, PhD

Senior Laboratory Manager
Laura Levi, PhD

Scientific programmer:
Jorrit Boekel, PhD

Scientific coordinator:
Helena Bäckvall, PhD

Global Proteomics and Proteogenomics

Proteogenomics is rapidly developing 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. The facility also provides service in broad range of MS-based proteomics applications to encompass the needs of the Swedish life science community, including quantitative proteomics and proteome profiling, in-depth proteomics, interaction studies by immunoprecipition MS (IP-MS) and post-translational modification (PTM) analysis.

Contacts and service requests through: iLAB platform at KI

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

Proteogenomics 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.

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

Start-up meeting and Experimental planning
Our long experience in applied proteomics provide us with a unique opportunity to assist users and in many instances refine the original experimental plan. For this reason we always offer a start-up meeting to go through the user request in detail.

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)


Mass spectrometers

MS Q Exactive HF, Thermo Scientific

MS Q Exactive HF, Thermo Scientific.

MS Orbitrap Exploris 480, Thermo Scientific.

MS Orbitrap Exploris 480, Thermo Scientific.

MS Tims-TOF pro, Bruker

MS TimsTOF HT incl Evoep, Bruker

MS Tims-TOF SCP incl Evosep, Bruker

Peptide separation technologies

HiRIEF (High Resolution Isoelectric Focusing)

Thermo Vanquish Neo LC


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

Pi-pet Sampleprep (modified Tecan Xantus), LAT

Delivery address

Masspektrometri, alfa plan 1
Tomtebodavägen 23 B
171 65 Solna

Visiting address

Tomtebodav 23A
171 65 Solna

Last updated: 2024-02-19

Content Responsible: Xenia Villalobos(