Chemical Proteomics

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SciLifeLab Infrastructure Unit Since 2017.

Primary: Shown in the list of current labels, if end date is not specified.

Started: 2017

Ended: Current

Year 2024

PubMed DOI Crossref
One-Pot Time-Induced Proteome Integral Solubility Alteration Assay for Automated and Sensitive Drug-Target Identification.
Meng Z, Saei AA, Lyu H, Gaetani M, Zubarev RA
Anal. Chem. - (-) - [2024-11-20; online 2024-11-20]
Chemical Proteomics [Technology development]
PubMed DOI Crossref
Merging multi-omics with proteome integral solubility alteration unveils antibiotic mode of action.
Maity R, Zhang X, Liberati FR, ..., Aínsa JA, Sancho J
Elife 13 (-) - [2024-09-27; online 2024-09-27]
Chemical Proteomics [Collaborative]
PubMed DOI Crossref
Gel-Assisted Proteome Position Integral Shift Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Caspase 3 Substrates.
Meng Z, Saei AA, Gharibi H, ..., Gaetani M, Zubarev RA
Anal. Chem. 96 (33) 13533-13541 [2024-08-20; online 2024-08-07]
Chemical Proteomics [Technology development]
PubMed DOI Crossref
Multifaceted Proteome Analysis at Solubility, Redox, and Expression Dimensions for Target Identification.
Saei AA, Lundin A, Lyu H, ..., Gygi SP, Zubarev RA
Adv Sci (Weinh) - (-) e2401502 [2024-08-09; online 2024-08-09]
Chemical Proteomics [Technology development]
PubMed DOI Crossref
A chemical inhibitor of IST1-CHMP1B interaction impairs endosomal recycling and induces noncanonical LC3 lipidation.
Knyazeva A, Li S, Corkery DP, ..., Waldmann H, Wu YW
Proc. Natl. Acad. Sci. U.S.A. 121 (17) e2317680121 [2024-04-23; online 2024-04-18]
Chemical Proteomics [Collaborative] Cryo-EM [Service]
PubMed DOI Crossref
Dual molecule targeting HDAC6 leads to intratumoral CD4+ cytotoxic lymphocytes recruitment through MHC-II upregulation on lung cancer cells.
Ducellier S, Demeules M, Letribot B, ..., Nascimento M, Apcher S
J Immunother Cancer 12 (4) - [2024-04-11; online 2024-04-11]
Chemical Proteomics [Collaborative]
PubMed DOI Crossref
Ultralight Ultrafast Enzymes.
Zhang X, Meng Z, Beusch CM, ..., Gaetani M, Zubarev RA
Angew. Chem. Int. Ed. Engl. 63 (3) e202316488 [2024-01-15; online 2023-12-07]
Chemical Proteomics [Collaborative]
PubMed DOI Crossref
Distinct molecular targets of ProEGCG from EGCG and superior inhibition of angiogenesis signaling pathways for treatment of endometriosis.
Hung SW, Gaetani M, Li Y, ..., Zubarev RA, Wang CC
J Pharm Anal 14 (1) 100-114 [2024-01-00; online 2023-09-11]
Chemical Proteomics [Collaborative]

Year 2023

DOI Crossref
Chemogenetic inhibition of IST1-CHMP1B interaction impairs endosomal recycling and promotes unconventional LC3 lipidation at stalled endosomes
Knyazeva A, Li S, Corkery DP, ..., Waldmann H, Wu YW
- - (-) - [2023-08-28; online 2023-08-28]
Chemical Proteomics [Collaborative]
PubMed DOI Crossref
Proteome integral solubility alteration high-throughput proteomics assay identifies Collectin-12 as a non-apoptotic microglial caspase-3 substrate.
Grabert K, Engskog-Vlachos P, Škandík M, ..., Joseph B, Cheray M
Cell Death Dis 14 (3) 192 [2023-03-11; online 2023-03-11]
Chemical Proteomics [Collaborative]
PubMed DOI Crossref
NCF1-dependent production of ROS protects against lupus by regulating plasmacytoid dendritic cell development and functions.
Luo H, Urbonaviciute V, Saei AA, ..., Zubarev RA, Holmdahl R
JCI Insight - (-) - [2023-02-28; online 2023-02-28]
Chemical Proteomics [Collaborative]

Year 2022

PubMed DOI Crossref
DAR 16-II Primes Endothelial Cells for Angiogenesis Improving Bone Ingrowth in 3D-Printed BCP Scaffolds and Regeneration of Critically Sized Bone Defects.
Alfayez E, Veschini L, Dettin M, ..., Coward T, Di Silvio L
Biomolecules 12 (11) 1619 [2022-11-02; online 2022-11-02]
Chemical Proteomics [Collaborative]
PubMed DOI Crossref
Proteomics-Compatible Fourier Transform Isotopic Ratio Mass Spectrometry of Polypeptides.
Gharibi H, Chernobrovkin AL, Saei AA, ..., Makarov AA, Zubarev RA
Anal. Chem. 94 (43) 15048-15056 [2022-11-01; online 2022-10-17]
Chemical Proteomics [Technology development]
PubMed DOI Crossref
Proteome Integral Solubility Alteration (PISA) for High-Throughput Ligand Target Deconvolution with Increased Statistical Significance and Reduced Sample Amount.
Gaetani M, Zubarev RA
Methods Mol. Biol. 2554 (-) 91-106 [2022-10-01; online 2022-10-01]
Chemical Proteomics [Technology development]
DOI Crossref
Mapping the GALNT1 substrate landscape with versatile proteomics tools
Saei AA, Lundström SL, Lyu H, ..., Gygi SP, Zubarev RA
- - (-) - [2022-08-24; online 2022-08-24]
Chemical Proteomics [Collaborative]
PubMed DOI Crossref
Ultrafast and selective labeling of endogenous proteins using affinity-based benzotriazole chemistry.
Xin X, Zhang Y, Gaetani M, ..., Corkery DP, Wu Y
Chem. Sci. 13 (24) 7240-7246 [2022-06-22; online 2022-05-30]
Chemical Proteomics [Collaborative]
PubMed DOI Crossref
Hepatocyte Thorns, A Novel Drug-Induced Stress Response in Human and Mouse Liver Spheroids.
Pridgeon CS, Bolhuis DP, Milosavljević F, ..., Jukić MM, Ingelman-Sundberg M
Cells 11 (10) - [2022-05-10; online 2022-05-10]
Chemical Proteomics [Collaborative]
PubMed DOI Crossref
The antimicrobial drug pyrimethamine inhibits STAT3 transcriptional activity by targeting the enzyme dihydrofolate reductase.
Heppler LN, Attarha S, Persaud R, ..., Page BDG, Frank DA
J. Biol. Chem. 298 (2) 101531 [2022-02-00; online 2021-12-23]
Chemical Proteomics [Collaborative]
PubMed DOI Crossref
Proteome Integral Solubility Alteration (PISA) Assay in Mammalian Cells for Deep, High-Confidence, and High-Throughput Target Deconvolution
Zhang X, Lytovchenko O, Lundström S, Zubarev R, Gaetani M
BIO-PROTOCOL 12 (22) - [2022-00-00; online 2022-00-00]
Chemical Proteomics [Technology development]

Year 2021

Proteome Integral Solubility Alteration (PISA) for High-Throughput Ligand Target Deconvolution with Increased Statistical Significance and Reduced Sample Amount (Book chapter)
Gaetani_M_and_Zubarev_RA
Methods in Molecular Biology in press (-) - [2021-12-09]
Chemical Proteomics [Technology development]
PubMed DOI Crossref
An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation.
Sabatier P, Beusch CM, Saei AA, ..., Rodin S, Zubarev RA
Nat Commun 12 (1) 6558 [2021-11-12; online 2021-11-12]
Chemical Proteomics [Technology development]
PubMed DOI Crossref
System-wide identification and prioritization of enzyme substrates by thermal analysis.
Saei AA, Beusch CM, Sabatier P, ..., Schüler H, Zubarev RA
Nat Commun 12 (1) 1296 [2021-02-26; online 2021-02-26]
Chemical Proteomics [Technology development]

Year 2020

PubMed DOI Crossref
Capillary leakage provides nutrients and antioxidants for rapid pneumococcal proliferation in influenza-infected lower airways.
Sender V, Hentrich K, Pathak A, ..., Normark S, Henriques-Normark B
Proc. Natl. Acad. Sci. U.S.A. 117 (49) 31386-31397 [2020-12-08; online 2020-11-23]
Bioinformatics Support for Computational Resources [Service] Chemical Proteomics [Collaborative]
PubMed DOI Crossref
Lysine-specific demethylase 1A restricts ex vivo propagation of human HSCs and is a target of UM171.
Subramaniam A, Žemaitis K, Talkhoncheh MS, ..., Zubarev RA, Larsson J
Blood 136 (19) 2151-2161 [2020-11-05; online 2020-06-26]
Bioinformatics Support for Computational Resources [Service] Chemical Proteomics [Collaborative]
PubMed DOI Crossref
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, ..., Zubarev R, Selivanova G
Cancer Res. 80 (7) 1538-1550 [2020-04-01; online 2020-02-04]
Chemical Proteomics [Collaborative]

Year 2019

PubMed DOI Crossref
ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery
Saei AA, Beusch CM, Chernobrovkin A, ..., Végvári Á, Zubarev RA
Nat Commun 10 (1) 5715 [2019-12-00; online 2019-12-16]
Chemical Proteomics [Technology development]
PubMed DOI Crossref
Proteome Integral Solubility Alteration: A High-Throughput Proteomics Assay for Target Deconvolution.
Gaetani M, Sabatier P, Saei AA, ..., Lundström SL, Zubarev RA
J. Proteome Res. 18 (11) 4027-4037 [2019-11-01; online 2019-10-14]
Chemical Proteomics [Technology development]
DOI Crossref
Functional Identification of Target by Expression Proteomics (FITExP)
Gaetani M, Zubarev RA
- - (-) 257-266 [2019-08-13; online 2019-07-26]
Chemical Proteomics [Technology development]
PubMed DOI Crossref
SpotLight Proteomics-A IgG-Enrichment Phenotype Profiling Approach with Clinical Implications.
Lundström SL, Heyder T, Wiklundh E, ..., Grunewald J, Zubarev RA
Int J Mol Sci 20 (9) 2157 [2019-05-01; online 2019-05-01]
Chemical Proteomics [Technology development]

Year 2018

PubMed DOI Crossref
Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation.
Visnes T, Cázares-Körner A, Hao W, ..., Boldogh I, Helleday T
Science 362 (6416) 834-839 [2018-11-16; online 2018-11-18]
Bioinformatics Support for Computational Resources [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Chemical Proteomics [Collaborative] Drug Discovery and Development (DDD) [Service] Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
STAT3 differential scanning fluorimetry and differential scanning light scattering assays: Addressing a missing link in the characterization of STAT3 inhibitor interactions.
Desroses M, Busker S, Astorga-Wells J, ..., Grandér D, Page BDG
Journal of Pharmaceutical and Biomedical Analysis 160 (-) 80-88 [2018-10-25; online 2018-07-17]
Chemical Proteomics [Collaborative] Protein Science Facility (PSF) [Service]

Year 2017

DOI Crossref
New Promises of Chemical Proteomics for Drug Development
Gaetani M, Zubarev RA
Novel Approaches in Drug Designing & Development 2 (1) 555579 [2017-06-27]
Chemical Proteomics [Technology development]
PubMed DOI Crossref
SpotLight Proteomics: uncovering the hidden blood proteome improves diagnostic power of proteomics.
Lundström SL, Zhang B, Rutishauser D, Aarsland D, Zubarev RA
Sci Rep 7 (-) 41929 [2017-02-07; online 2017-02-07]
Chemical Proteomics [Technology development]

Year 2016

PubMed DOI Crossref
Human IgM Antibodies to Malondialdehyde Conjugated With Albumin Are Negatively Associated With Cardiovascular Disease Among 60-Year-Olds.
Thiagarajan D, Frostegård AG, Singh S, ..., Lundström SL, Frostegård J
J Am Heart Assoc 5 (12) - [2016-12-20; online 2016-12-20]
Chemical Proteomics [Collaborative]
PubMed DOI Crossref
Validation and development of MTH1 inhibitors for treatment of cancer.
Warpman Berglund U, Sanjiv K, Gad H, ..., Scobie M, Helleday T
Ann. Oncol. 27 (12) 2275-2283 [2016-12-00; online 2016-11-08]
Advanced Mass Spectrometry Proteomics [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Chemical Proteomics [Service] Clinical Proteomics Mass spectrometry [Collaborative] Drug Discovery and Development (DDD) [Collaborative]
PubMed DOI Crossref
Application of amide hydrogen/deuterium exchange mass spectrometry for epitope mapping in human cystatin C.
Prądzińska M, Behrendt I, Astorga-Wells J, ..., Rodziewicz-Motowidło S, Czaplewska P
Amino Acids 48 (12) 2809-2820 [2016-12-00; online 2016-08-29]
Advanced Mass Spectrometry Proteomics [Collaborative] Chemical Proteomics [Collaborative]
PubMed DOI Crossref
Functional and Structural Characterization of a Novel HLA-DRB1*04:01-Restricted α-Enolase T Cell Epitope in Rheumatoid Arthritis.
Gerstner C, Dubnovitsky A, Sandin C, ..., Achour A, Malmström V
Front Immunol 7 (-) 494 [2016-11-14; online 2016-11-14]
Chemical Proteomics [Service]
PubMed DOI Crossref
Isolation and characterization of autoantibodies against human cystatin C.
Prądzińska M, Behrendt I, Spodzieja M, ..., Macur K, Czaplewska P
Amino Acids 48 (11) 2501-2518 [2016-11-00; online 2016-06-08]
Advanced Mass Spectrometry Proteomics [Collaborative] Chemical Proteomics [Collaborative]
PubMed DOI Crossref
Establishing a Proteomics-Based Monocyte Assay To Assess Differential Innate Immune Activation Responses.
Tarasova NK, Ytterberg AJ, Lundberg K, ..., Harris RA, Zubarev RA
J. Proteome Res. 15 (7) 2337-2345 [2016-07-01; online 2016-06-03]
Advanced Mass Spectrometry Proteomics [Collaborative] Chemical Proteomics [Technology development]
PubMed DOI Crossref
DeMix-Q: Quantification-Centered Data Processing Workflow.
Zhang B, Käll L, Zubarev RA
Mol. Cell Proteomics 15 (4) 1467-1478 [2016-04-00; online 2016-01-04]
Chemical Proteomics [Technology development]

Year 2015

PubMed DOI Crossref
Functional Identification of Target by Expression Proteomics (FITExP) reveals protein targets and highlights mechanisms of action of small molecule drugs.
Chernobrovkin A, Marin-Vicente C, Visa N, Zubarev RA
Sci Rep 5 (-) 11176 [2015-06-08; online 2015-06-08]
Advanced Mass Spectrometry Proteomics Chemical Proteomics [Technology development]
SciLifeLab Data Centre
Publications 9.5.1