Clinical Proteomics Mass Spectrometry core facility

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.

Services during holidays:

The core facility 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)

Head of the facility:

Lukas Orre, PhD, Associate Professor and Principal Researcher

Karolinska Institutet, Department of Oncology-Pathology

Lukas.orre@ki.se