Chemical Proteomics Core Facility

The Chemical Proteomics facility (ChemProt) is a recent national facility expert on supporting drug discovery and development by proteome-wide deconvolution of targets and mechanism of action (MoA) of small molecules or any active compounds.

ChemProt is the reference facility for chemical proteomics within SciLifeLab and BioMS national infrastructures.

The main goal of ChemProt is to decipher proteome signatures induced by an active compound for MoA elucidation and target identification. For these aims, ChemProt has adopted the latest mass spectrometry(MS)-based proteomic technologies and developed new high-throughput (HT) methods.

ChemProt also provides the HDX-MS (hydrogen-deuterium exchange mass spectrometry) technology for protein structure analysis on purified proteins with the goal of mapping the site of interaction with active compound of conformational changes in response to the applied system perturbation.

Using multidisciplinary competences and resources, ChemProt represents an innovative facility model offering complete pipelines from perturbations in cell cultures, to MS-based proteomics and data analysis, including data bioinformatics processing, publication figures and data representation.

ChemProt has recently developed high throughput (HT) chemical proteomics methods which outperforms the previous methods for target deconvolution of at least tenfold and decreases 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.

Instruments of the Chemical Proteomics Core Facility.

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.

Summary of Current Technologies and Services

A) Chemical Proteomics for Target Discovery and Determination of Mechanism of Action (MoA) and Off-Target landscape

A1) Orthogonal methods of deep mass spectrometry-based proteomics based on

  • 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 (the first three are developed in-house):

  • Proteome Integral Solubility Alteration (PISA) Assayhigh throughput method based on protein solubility/stability upon thermal treatment (J Proteome Res 2019, DOI: 1021/acs.jproteome.9b00500) with no need of chemical engineering of compounds (now up to 16-plex with TMTpro 16-plex, i.e. 16 biological samples in one multiplex analysis);
  • FITExP, based on compound-specific proteome responses (Sci Rep 2015, DOI: 1038/srep11176) and with no need of chemical engineering of compounds (now up to 16-plex with TMTpro 16-plex)
  • ProTargetMinerhigh throughput method to study anticancer compounds based on FITExP-derived database of proteome signatures using a library of anticancer molecules (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 with TMTpro 16-plex)
  • Thermal Proteome Profiling (TPP), based on protein melting curve fitting and Tm extrapolation (Nat Commun 2019, DOI: 1126/science.1255784)
  • RedOx Proteomics, for specific proteome changes in the reduction-oxidation balance

A2) “System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis” (SIESTA), a new method developed in-house (Nat Commun 2021, DOI: 10.1038/s41467-021-21540-6) for identification of enzyme protein substrates. It relyes on the enzymatic post-translational modifications of substrate proteins changing their solubility and it assesses solubility changes of proteins in cell lysate when a recombinant protein and a co-factor are simultaneously added to the lysate in excess.

A3) Additional proteomics services related to / coordinated with the above (e.g. PTMs, deep quantitative proteomics, etc.)

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

HDX-MS workflows are optimized at ChemProt for:

B1) Binding site mapping and characterization for: protein-small molecule interactions; protein-peptide interactions; protein-protein interactions, including epitope mapping;

B2) Conformational changes monitoring to study effects of mutations, to analyze misfolding and for biosimilar characterization

Equipment

ChemProt laboratories are at located at Biomedicum, Karolinska Institutet. 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

Data Analysis Harware and Software:

Four PC stations, Proteome Discoverer 2.4, BioPharma Finder, Peaks, MaxQuant, Mascot, SIMCA, GraphPad PRISM, Excel, R, etc.

Instruments of the Chemical Proteomics Core Facility.
Instruments of the Chemical Proteomics Core Facility.
Instruments of the Chemical Proteomics Core Facility.
Instruments of the Chemical Proteomics Core Facility.
Instruments of the Chemical Proteomics Core Facility.

Recent Projects

System-wide identification and prioritization of enzyme substrates by thermal analysis.
Saei AA, Beusch CM, Sabatier P, Wells JA, Gharibi H, Meng Z, Chernobrovkin A, Rodin S, Näreoja K, Thorsell AG, Karlberg T, Cheng Q, Lundström SL, Gaetani M, Végvári Á, Arnér ESJ, Schüler H, Zubarev RA
Nat Commun 2021 02;12(1):1296

Capillary leakage provides nutrients and antioxidants for rapid pneumococcal proliferation in influenza-infected lower airways.
Sender V, Hentrich K, Pathak A, Tan Qian Ler A, Embaie BT, Lundström SL, Gaetani M, Bergstrand J, Nakamoto R, Sham LT, Widengren J, Normark S, Henriques-Normark B
Proc Natl Acad Sci U S A 2020 12;117(49):31386-31397

Lysine-specific demethylase 1A restricts ex vivo propagation of human HSCs and is a target of UM171.
Subramaniam A, Žemaitis K, Talkhoncheh MS, Yudovich D, Bäckström A, Debnath S, Chen J, Jain MV, Galeev R, Gaetani M, Zubarev RA, Larsson J
Blood 2020 Nov;136(19):2151-2161

Thermal Proteome Profiling Identifies Oxidative-Dependent Inhibition of the Transcription of Major Oncogenes as a New Therapeutic Mechanism for Select Anticancer Compounds.
Peuget S, Zhu J, Sanz G, Singh M, Gaetani M, Chen X, Shi Y, Saei AA, Visnes T, Lindström MS, Rihani A, Moyano-Galceran L, Carlson JW, Hjerpe E, Joneborg U, Lehti K, Hartman J, Helleday T, Zubarev R, Selivanova G
Cancer Res 2020 04;80(7):1538-1550

ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery.
Saei AA, Beusch CM, Chernobrovkin A, Sabatier P, Zhang B, Tokat ÜG, Stergiou E, Gaetani M, Végvári Á, Zubarev RA
Nat Commun 2019 12;10(1):5715

Proteome Integral Solubility Alteration: A High-Throughput Proteomics Assay for Target Deconvolution.
Gaetani M, Sabatier P, Saei AA, Beusch CM, Yang Z, Lundström SL, Zubarev RA
J Proteome Res 2019 11;18(11):4027-4037

Using the Facility

Please feel free to contact us (massimiliano.gaetani@ki.se) and come visit us at KI Biomedicum. You will receive consultation free of charge, finding out about feasibility, details and better solutions for your project or your potential one.

From the 8th of April 2021 Chemical Proteomics is available under the iLab system for KI core facilities. Our users are required to log in iLab , and submit a project request to Chemical Proteomics. Please contact us for any questions.

ChemProt is also the national facility expert of Chemical Proteomics within the Swedish infrastructure for biological mass spectrometry (BioMS). ChemProt is responsible for the entire Chemical Proteomics technology and also provider of protein structural analysis through HDX-MS. Through BioMS and SciLifeLab we can support your project and cover relevant costs of it by national funding. The users will be instructed on how to register services to our facility also through an application at the BioMS portal for the "Chemical Proteomics” technology.

Guidelines

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.

User fees

A) Chemical proteomics services for target deconvolution and MoA Identification are provided as full pipeline, including

  • Consultation, project description generation and experiment design (free of charge)
  • Cell culture and drug / compound treatments
  • Cells / tissue sample processing
  • Sample preparation for mass spectrometry-based proteomics
  • Tandem Mass Tag (TMT) reporter ion labelling for multiplexed quantitative proteomics. Up to 16 biological replicates in one multiplexed experiment and coordination of multiplexed experiments are available
  • Sample fractionation for deep analysis 
  • nLC-MS analysis of samples / sample fractions
  • MS-based protein identification and quantification
  • Functional data analysis and interpretation
  • Consultation and follow-up support for publications and further experimental design (free of charge)

The final price to the user is given for the whole pipeline considering only effective runs generating research data. Repeated runs for technical problems and pilot experiments are free of charge.

To address the need of different levels of proteomics depths in different projects, we have differentiated different levels of prices depending on the LC-MS instrument time and fractions (F) analyzed for the project.

Each third-party cost, such as cell lines or primary cells and compound purchased for the customer on request, will be added on the top of the final cost of the service.

Prices below are related to one multiplex format, up to 16 replicates. For higher number of samples, more than one multiplex will apply. Users from university benefit from a high level of subsidy, even higher for internal KI users, while industry is charged full cost. Prices for KI Users (KI), External (E) and Industry (I) are shown below.

PISA (up to 16 total replicates)
PISA (up to 16 total replicates) KI users External Industry
48F_Protein depth: very high (> 8500 ID): 75 tKr 90 tKr 247 tKr
24F_Protein depth: high (> 7000 ID) 55 tKr 66 tKr 192.5 tKr
12F_Protein depth: medium (>5000 ID): 35 tKr 42 tKr 122.5 tKr
6F_ only proteomes of <3K proteins 26 tKr 31.2 tKr 91 tKr
PISA-Express (up to 16 total replicates)
PISA-Express (up to 16 total replicates) KI users External Industry
48F_Protein depth: very high (>9500 ID): 75 tKr 90 tKr 247 tKr
24F_Protein depth: high (> 8000 ID) 55 tKr 66 tKr 193 tKr
12F_Protein depth: medium (>5000 ID): 35 tKr 42 tKr 123 tKr
6F_ only proteomes of <3K proteins 26 tKr 31.2 tKr 91 tKr
Expression Proteomics / FITEXP / ProTargetMiner (up to 16 total replicates)
Expression Proteomics / FITEXP / ProTargetMiner (up to 16 total replicates) KI users External Industry
48F_Protein depth: very high (>9500 ID): 70 tKr 84 tKr 231 tKr
24F_Protein depth: high (> 8000 ID) 50 tKr 60 tKr 175 tKr
12F_Protein depth: medium (> 5000 ID): 30 tKr 30 tKr 105 tKr
6F_ only proteomes of <3K proteins 20 tKr 24 tKr 70 tKr
SIESTA (up to 16 total replicates)
SIESTA (up to 16 total replicates)
Please refer to PISA prices.

The prices of the new incoming services will be built of the bases of the one above, related to the multiplex TMT with added costs that will be evaluated after method optimization.

B) HDX-MS services: prices are related per one protein with one ligand (e.g. small molecule or antibody in case of epitope mapping). The first step is always a feasibility experiment, to assess if a good sequence coverage is reached. Then full HDX-MS experiment using protein alone or plus ligand is performed with a standard of 3-4 time points. Each additional ligand on the same protein can be added at lower costs.

Hydrogen Deuterium exchange mass spectrometry (HDX-MS)
Hydrogen Deuterium exchange mass spectrometry (HDX-MS) KI users External Industry
Feasibility: 10 tKr 12 tKr 33 tKr
1st experiment one protein + 1st ligand 40 tKr 48 tKr 140 tKr
Each additional ligand: 10 tKr 12 tKr 33 tKr

Access for qualified personel

Only for qualified personnel, it is possible to have access to LC-MS/MS instrumentation for chemical proteomics experiment performed directly by the user, for minimum 4 consecutive hours and with a mandatory initial start-up charge.

Expert User running LC-MS/MS for chemical proteomics
Expert User running LC-MS/MS for chemical proteomics KI users External Industry
Start-up charge: 3000 Kr 3600 Kr 4500 Kr
Q Exactive HF and HF-X: 500 Kr/h 600 Kr/h 750 Kr/h
Fusion Tribrid with ETD: 550 Kr/h 660 Kr/h 825 Kr/h
Lumos Tribrid: 600 Kr/h 720 Kr/h 900 Kr/h

Visiting Address

Karolinska Institutet
Department of Medical Biochemistry and Biophysics (MBB)
Biomedicum, quarter A9, floor 9
Solnavägen 9
Stockholm, Sweden

Contact

Personnel

Roman Zubarev, Ph.D. (Facility Director)
Massimiliano Gaetani, Ph.D. (Head of Facility)
Susanna Lundström, Ph.D. (Senior Staff Proteomics Specialist)
Olga Lytovchenko, Ph.D. (Staff Research Engineer)
Zhaowei Meng (Staff LC-MS Engineer)
Qinyu Jia (Associated HDX-MS Specialist)
Pan Fang, Ph.D. (Staff HDX-MS Research Engineer)
Giorgia Palano, Ph.D (Staff Research Engineer- Stem Cells and 3D cultures)