Clinical Proteomics Mass Spectrometry core facility

Clinical Proteomics Mass Spectrometry (MS) is a core facility that offers you an opportunity to analyze the proteome composition of biological samples. The facility provides expertise and services in a wide range of MS-based proteomics methods with focus on in-depth quantitative proteomics and clinical proteomics. The facility also offers expert support
in experimental design as well as downstream data analysis to ensure a high quality service.

We continuously strive to develop and implement cutting edge research methods in our services. This is exemplied by the level of data produced by the HiRIEF method used for in-depth proteomics, and by our continuous development of bioinformatics methods for optimal use of the generated data. The financial support for the facility is provided by the Stockholm county council (SLL).

Services offered

Services offered

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.

Clinical proteomics

We have a long experience of clinical proteomics projects including a wide variety of different human tissues and body fluids. In many cases the sample preparation procedures needs to be tailored for the specific samples and we will assist you in this crucial part of the project. In optimal cases we are involved from early phases of the project to ensure that sample collection is optimal for downstream proteomics analysis.

In-depth proteomics

Analytical depth is key to understand biology in all of its complexity. Based on our in-house developed methods for improved analytical depth in proteomics experiments (HiRIEF), we are able to offer state-of-the-art coverage of the proteome. In a fully complex sample this often results in the identification of more than 10 000 unique proteins.

Quantitative proteomics

In most proteomics applications the primary interest is to compare the abundance of proteins between samples. This requires sensitive and accurate quantification of protein levels between samples. We apply both multiplexed methods like TMT and label-free methods for quantitative proteomics. In particular, our HiRIEF method is perfectly integrated with multiplexed methods to generate accurate relative quantification of thousands of proteins in up to 10 samples in a single experiment.

PTM analysis

The functional state of proteins is heavily dependent on the addition of functional groups, so-called post translational modifications (PTMs), to the primary amino-acid sequence. Therefore, it is often important to investigate the protein PTMs, such as for example phosphorylations. Such analysis typically requires specialized sample preparation including enrichment strategies, and we can help with guiding users among these applications.

Plasma proteomics

We use our HiRIEF method for robust and in-depth quantification of proteins in plasma. From 40 uL non-depleted plasma we profile on average > 1000 proteins over large sets of clinical samples.

Protein identification

In a range of different applications, the primary interest is the qualitative identification of the proteins that are present in a biological sample. Examples of such applications are protein interaction studies and protein complex studies. These samples are often of lower complexity, but with limited amount of starting material and consequently we adapt the experimental setup accordingly.

Bioinformatics

All projects we take on are offered free of charge expert assistance with experimental design. Further, project reports include normalized, analysis ready result output and a QC-report. For the downstream proteomics data analysis, we offer statistical analysis and data visualization, charged by an hourly rate according to the scope of the project. Examples of statistical analyses offered are differential analysis by both standard (t-test) and proteomics-specific (DEqMS) methods, presented in volcano plots. Other analyses include clustering visualized by heatmaps, principal components analysis (PCA) and biological characterization in terms of gene ontology enrichment analyses or gene set enrichment analyses (GSEA).

Equipment

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.

 

Robotic sample preparation

Ettan Digester, GE Healthcare Life Science

Pi-pet Sampleprep, LAT (Laboratory Automation Technology)

Peptide separation technologies

HiRIEF (High resolution isoelectric focusing)

Liquid Chromatography (UPLC/HPLC/FPLC).

 

Further reading

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.
Branca RM, Orre LM, Johansson HJ, Granholm V, Huss M, Pérez-Bercoff Å, et al
Nat. Methods 2014 Jan;11(1):59-62.
 

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.
Zhu Y, Orre LM, Johansson HJ, Huss M, Boekel J, Vesterlund M, et al
Nat Commun 2018 03;9(1):903
 

DEqMS: a method for accurate variance estimation in differential protein expression analysis.
Zhu Y, Orre LM, Zhou Tran Y, Mermelekas G, Johansson HJ, Malyutina A, et al
Mol. Cell Proteomics 2020 Mar;():

In-depth human plasma proteome analysis captures tissue proteins and transfer of protein variants across the placenta.
Pernemalm M, Sandberg A, Zhu Y, Boekel J, Tamburro D, Schwenk JM, et al
Elife 2019 04;8():

Visiting address

SciLifeLab Alpha floor 1, Mass Spectrometry

Tomtebodavägen 23a

17165 Solna, Sweden

 

Contact

Project requests: proteomicscore@scilifelab.se

Lukas Orre

Head of the facility:

Lukas Orre, PhD, Senior Researcher

Karolinska Institutet, Department of Oncology-Pathology

Lukas.orre@ki.se

Personnel

Facility Director:

Prof. Janne Lehtiö, PhD

Head of Facility:

Lukas Orre, PhD

Research engineers:

Ghazaleh Assadi, PhD

Xiaofang Cao, PhD

Georgios Mermelekas, PhD

Kaveh Moazemi-Goudarzi, PhD

Mohammad Pirmoradian, PhD

Eduardo Araújo, PhD

Scientists:

Rui Branca, PhD

Rozbeh Jafari, PhD

Henrik Johansson, PhD

Maria Pernemalm, PhD

Mattias Vesterlund, PhD

Scientific programmer:

Jorrit Boekel, PhD

Bioinformatician:

AnnSofi Sandberg, PhD

Scientific coordinator:

Helena Bäckvall, PhD

Core facility interior

Interior of clinical proteomics mass spectrometry core facility.
Interior of clinical proteomics mass spectrometry core facility
Interior of clinical proteomics mass spectrometry core facility