Chemical Proteomics

Part of the Chemical Proteomics and Proteogenomics facility

The Chemical Proteomics facility (ChemProt) is a national facility expert on supporting drug discovery and development by proteome-wide deconvolution of targets and action mechanisms of small molecules.

ChemProt has recently developed high throughput (HT) chemical proteomics methods which outperform the previous methods for target deconvolution of at least tenfold and decrease by the same factor the time of analysis of the sample amount needed for each biological replicate. The novel methods can use a high level on multiplexing for several biological replicates, up to 16 per experiment according to the latest state of the art for quantitative proteomics. Different compounds or more than one biological system can be tested simultaneously. The LC-MS instrument park has been renewed  for better supporting the new high throughput chemical proteomics.

Useful links

• National BioMS infrastructure and Chemical Proteomics technology
• ChemProt website at Karolinska Institutet 

Services

ChemProt makes use of proteome-wide orthogonal approaches to find out how small molecules work when incubated in cell cultures and in lysates. Most approaches can be provided with no molecular modification for chemical probe engineering. ChemProt can provide full pipelines reproducing the biological treatments of the phenotype of interest or operating the treatment planned with the users.  ChemProt also offers hydrogen-deuterium exchange mass spectrometry (HDX-MS) for mapping and characterizing the target binding site, and monitoring other structural changes. Our outcomes include full data analysis, high confidence identification of most reproducible and treatment-specific MoA signatures and target candidates. Follow up support for consequent experimental and publication purposes are provided; consultation is always provided on request and free of charge, also to guide further planning.

Current Technologies and Services

Deconvolution of compound targets, determination of mechanism of Action (MoA) and off-target landscape through orthogonal methods of mass spectrometry-based deep proteomics

• protein solubility/stability alteration signatures in treated cell cultures and lysates;
• treatment-specific expression/degradation proteome signatures;
• changes in proteome redox balance in treated cell cultures.

Matches over two orthogonal approaches dramatically increase the chances to find the correct target. These methods are here listed:

• Proteome Integral Solubility Alteration (PISA) Assay, high throughput method based on protein solubility/stability upon thermal treatment, with no need of chemical engineering of compounds (now up to 16-plex, i.e. 16 biological samples in one multiplex analysis) (Gaetani M et al., J Proteome Res, 2019, DOI: 1021/acs.jproteome.9b00500);
• FITExP, based on compound-specific proteome responses and with no need of chemical engineering of compounds (now up to 16-plex) (Chernobrovkin A et al., Sci Rep, 2015, DOI:1038/srep11176 );
• ProTargetMiner, high throughput method to study anticancer compounds based on FITExP-derived database of proteome signatures using a library of anticancer molecules (Saei AA et al., Nat Commun, 2019; DOI:1038/s41467-019-13582-8);
• Identification of interactions and protein complexes after affinity-based approaches using chemical engineered probes (now up to 16-plex)
• Thermal Proteome Profiling (TPP), based on protein melting curve fitting and Tm extrapolation (Savitski MM et al., Science, 2014, DOI: 1126/science.1255784)
• RedOx Proteomics, for specific proteome changes in the reduction-oxidation balance

Protein Structural Analysis using Hydrogen-deuterium exchange mass spectrometry (HDX-MS)

• Binding site mapping and characterization for: protein-small molecule interactions; protein-peptide interactions; protein-protein interactions, including epitope mapping;
• Conformational changes monitoring to study effects of mutations, to analyze misfolding and for biosimilar characterization

Identification of enzyme protein substrates

Using a thermal profiling (TPP or PISA) based approach in cell lysate and recombinant enzymes and their co-factors (Saei AA et al, submitted; BioRxiv: DOI: 1101/423418 )

Additional proteomics services related to / coordinated with the above 

(e.g. PTMs, deep quantitative proteomics, etc.)

Equipment

ChemProt laboratories are at located at the Department of Medical Biochemistry and Biophysics (MBB) of Karolinska Institutet, Biomedicum. ChemProt represents an innovative facility model offering complete pipelines and including different laboratories for cell culture, sample preparation, LC-MS and bioinformatic analysis.

Cell culture lab Instruments: Two laminar flow cabinets, Two CO₂ incubators, Two Microscopes, Eppendorf centrifuge, BioRad cell counter, etc.

Centrifuges: Beckmann XPN-80 ultracentrifuge, Speedvac centrifuges , Eppendorf centrifuges for large and small tubes

Mass Spectrometers:

• Two Orbitrap Fusion Lumos, Thermo Scientific
• Two Orbitrap Q Exactives HF-X, Thermo Scientific
• One Orbitrap Fusion, Thermo Scientific
• Two Orbitrap Q Exactives HF, Thermo Scientific
• One Orbitrap Q Exactive, Thermo Scientific

UPLC:

• Two Ultimate 3000 RSLCnano for double column operation
• Five UltiMate 3000 RSLCnano / nEasy-LC 1000 for nLC-MS
• Ultimate 3000 for off-line high pH fractionation;
• Three UltiMate 3000 Nano LC or nEasy-LC 1000 for nLC-MS

HDX-MS Robot: CTC PAL Liquid Handling System connected to a Peltier-cooled box

Data Analysis Harware and Software: Four PC stations, Proteome Discoverer 2.4, BioPharma Finder, Peaks, MaxQuant, Mascot, SIMCA, GraphPad PRISM, Excel, R, etc.

General guidelines for using the facility

From October 1, 2020 new guidelines are applied, in line with the guidelines introduced by KI on 1/1/2018.

After an initial discussion of the project and before sample submission, the user is kindly requested to provide a brief description of the project and for that provided with a project description template and necessary help for its completion. The final project description will undergo internal facility approval and necessary suggestions to optimize the project design and maximize data quality and scientific impact of the facility application in the project.

The user could choose different levels of services, summarized below:

• Contract/service analysis: Research data acquisition. No data analysis or interpretation will be provided by facility. Archiving and public access is customer’s responsibility. No intellectual property will be retained by the facility. No authorship demand by facility. User fee will be applied.
• Collaborative analysis: Besides research data acquisition (for which the same user fee will be applied as in Contract/service analysis), data analysis and interpretation will be provided. Archiving and public access will be provided. Intellectual property about the analysis and its results will be shared and authorship will be shared (please see our Rules on Intellectual Property and Publications).

The facility can also be engaged with Collaborative research, meaning that the facility is part of a grant application together with the collaborator(s) and all costs are already defined and given upfront of the analysis after grant approval.