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For: Schoof EM, Furtwängler B, Üresin N, Rapin N, Savickas S, Gentil C, Lechman E, Keller UAD, Dick JE, Porse BT. Quantitative single-cell proteomics as a tool to characterize cellular hierarchies. Nat Commun 2021;12:3341. [PMID: 34099695 PMCID: PMC8185083 DOI: 10.1038/s41467-021-23667-y] [Citation(s) in RCA: 216] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023]  Open
Number Cited by Other Article(s)
1
Wang Z, Zhang T, Tang M. Navigating nanotoxicity: Unraveling nanomaterial-induced effects via multi-omics integration. NANOIMPACT 2025;38:100565. [PMID: 40383513 DOI: 10.1016/j.impact.2025.100565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2025] [Revised: 04/14/2025] [Accepted: 05/12/2025] [Indexed: 05/20/2025]
2
Su P, Hollas MAR, Pla I, Rubakhin S, Butun FA, Greer JB, Early BP, Fellers RT, Caldwell MA, Sweedler JV, Kafader JO, Kelleher NL. Proteoform profiling of endogenous single cells from rat hippocampus at scale. Nat Biotechnol 2025:10.1038/s41587-025-02669-x. [PMID: 40374954 DOI: 10.1038/s41587-025-02669-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/04/2025] [Indexed: 05/18/2025]
3
Tang C, Xu W, Chen Y, Yu H, Xu L, Zhang C, Zhang Y, Liang Y. DFT calculations guide the design of dual-responsive molecule 9,10-phenanthrenequinone-sydnone. Chem Commun (Camb) 2025. [PMID: 40357574 DOI: 10.1039/d5cc00819k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2025]
4
Leduc A, Xu Y, Shipkovenska G, Dou Z, Slavov N. Limiting the impact of protein leakage in single-cell proteomics. Nat Commun 2025;16:4169. [PMID: 40324992 PMCID: PMC12053607 DOI: 10.1038/s41467-025-56736-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Accepted: 01/28/2025] [Indexed: 05/07/2025]  Open
5
Petrosius V, Aragon-Fernandez P, Arrey TN, Woessman J, Üresin N, de Boer B, Su J, Furtwängler B, Stewart H, Denisov E, Petzoldt J, Peterson AC, Hock C, Damoc E, Makarov A, Zabrouskov V, Porse BT, Schoof EM. Quantitative Label-Free Single-Cell Proteomics on the Orbitrap Astral MS. Mol Cell Proteomics 2025:100982. [PMID: 40334743 DOI: 10.1016/j.mcpro.2025.100982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 03/26/2025] [Accepted: 04/23/2025] [Indexed: 05/09/2025]  Open
6
Kanao E, Ishihama Y. StageTip: a little giant unveiling the potential of mass spectrometry-based proteomics. ANAL SCI 2025;41:667-675. [PMID: 40138149 PMCID: PMC12064472 DOI: 10.1007/s44211-025-00749-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Accepted: 03/06/2025] [Indexed: 03/29/2025]
7
Gaizley EJ, Chen X, Bhamra A, Enver T, Surinova S. Multiplexed phosphoproteomics of low cell numbers using SPARCE. Commun Biol 2025;8:666. [PMID: 40287540 PMCID: PMC12033357 DOI: 10.1038/s42003-025-08068-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Accepted: 04/09/2025] [Indexed: 04/29/2025]  Open
8
Lin KT, Muneer G, Huang PR, Chen CS, Chen YJ. Mass Spectrometry-Based Proteomics for Next-Generation Precision Oncology. MASS SPECTROMETRY REVIEWS 2025. [PMID: 40269546 DOI: 10.1002/mas.21932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 03/29/2025] [Accepted: 04/01/2025] [Indexed: 04/25/2025]
9
Nitz A, Giraldez Chavez JH, Eliason ZG, Payne SH. Are We There Yet? Assessing the Readiness of Single-Cell Proteomics to Answer Biological Hypotheses. J Proteome Res 2025;24:1482-1492. [PMID: 38981598 PMCID: PMC11976870 DOI: 10.1021/acs.jproteome.4c00091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/02/2024] [Accepted: 06/13/2024] [Indexed: 07/11/2024]
10
Pang M, Jones JJ, Wang TY, Quan B, Kubat NJ, Qiu Y, Roukes ML, Chou TF. Increasing Proteome Coverage Through a Reduction in Analyte Complexity in Single-Cell Equivalent Samples. J Proteome Res 2025;24:1528-1538. [PMID: 38832920 PMCID: PMC11976869 DOI: 10.1021/acs.jproteome.4c00062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/23/2024] [Accepted: 05/14/2024] [Indexed: 06/06/2024]
11
Peters-Clarke TM, Liang Y, Mertz KL, Lee KW, Westphall MS, Hinkle JD, McAlister GC, Syka JEP, Kelly RT, Coon JJ. Boosting the Sensitivity of Quantitative Single-Cell Proteomics with Infrared-Tandem Mass Tags. J Proteome Res 2025;24:1539-1548. [PMID: 38713017 PMCID: PMC12068060 DOI: 10.1021/acs.jproteome.4c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
12
Cheung TK, Zhu Y, Rose CM. Offset Mass Carrier Proteome Improves Quantification of Multiplexed Single Cell Proteomics. Mol Cell Proteomics 2025;24:100959. [PMID: 40180178 PMCID: PMC12090233 DOI: 10.1016/j.mcpro.2025.100959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2024] [Revised: 03/06/2025] [Accepted: 03/30/2025] [Indexed: 04/05/2025]  Open
13
Sanchez-Avila X, de Oliveira RM, Huang S, Wang C, Kelly RT. Trends in Mass Spectrometry-Based Single-Cell Proteomics. Anal Chem 2025;97:5893-5907. [PMID: 40091206 PMCID: PMC12003028 DOI: 10.1021/acs.analchem.5c00661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
14
Mulvey JF, Meyer EL, Svenningsen MS, Lundby A. Integrating -Omic Technologies across Modality, Space, and Time to Decipher Remodeling in Cardiac Disease. Curr Cardiol Rep 2025;27:74. [PMID: 40116972 PMCID: PMC11928419 DOI: 10.1007/s11886-025-02226-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/11/2025] [Indexed: 03/23/2025]
15
Xie Y, Chen X, Xu M, Zheng X. Application of the Human Proteome in Disease, Diagnosis, and Translation into Precision Medicine: Current Status and Future Prospects. Biomedicines 2025;13:681. [PMID: 40149657 PMCID: PMC11940125 DOI: 10.3390/biomedicines13030681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Revised: 02/21/2025] [Accepted: 02/28/2025] [Indexed: 03/29/2025]  Open
16
Hernandez R, Garcia-Rodriguez NS, Arriaga MA, Perez R, Bala AA, Leandro AC, Diego VP, Almeida M, Parsons JG, Manusov EG, Galan JA. The hepatocellular model of fatty liver disease: from current imaging diagnostics to innovative proteomics technologies. Front Med (Lausanne) 2025;12:1513598. [PMID: 40109726 PMCID: PMC11919916 DOI: 10.3389/fmed.2025.1513598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Accepted: 02/06/2025] [Indexed: 03/22/2025]  Open
17
Kardassis D, Vindis C, Stancu CS, Toma L, Gafencu AV, Georgescu A, Alexandru-Moise N, Molica F, Kwak BR, Burlacu A, Hall IF, Butoi E, Magni P, Wu J, Novella S, Gamon LF, Davies MJ, Caporali A, de la Cuesta F, Mitić T. Unravelling molecular mechanisms in atherosclerosis using cellular models and omics technologies. Vascul Pharmacol 2025;158:107452. [PMID: 39667548 DOI: 10.1016/j.vph.2024.107452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Revised: 10/31/2024] [Accepted: 12/02/2024] [Indexed: 12/14/2024]
18
Li ZP, Du Z, Huang DS, Teschendorff AE. Interpretable deep learning of single-cell and epigenetic data reveals novel molecular insights in aging. Sci Rep 2025;15:5048. [PMID: 39934290 PMCID: PMC11814351 DOI: 10.1038/s41598-025-89646-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Accepted: 02/06/2025] [Indexed: 02/13/2025]  Open
19
Dutta S, Pang M, Coughlin GM, Gudavalli S, Roukes ML, Chou TF, Gradinaru V. Molecularly-guided spatial proteomics captures single-cell identity and heterogeneity of the nervous system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.10.637505. [PMID: 39990460 PMCID: PMC11844393 DOI: 10.1101/2025.02.10.637505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
20
Lecornec N, Duchmann M, Itzykson R. Single-cell sequencing applications in acute myeloid leukemia. Leuk Lymphoma 2025;66:175-189. [PMID: 39496597 DOI: 10.1080/10428194.2024.2422833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 09/26/2024] [Accepted: 10/23/2024] [Indexed: 11/06/2024]
21
Meteling M, Johnbosco C, Wolfel A, Conceição F, Govindaraj K, Moreira Teixeira L, Leijten J. High-Throughput Single-Cell Analysis of Local Nascent Protein Deposition in 3D Microenvironments via Extracellular Protein Identification Cytometry (EPIC). ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2025;37:e2415981. [PMID: 39629556 PMCID: PMC11817916 DOI: 10.1002/adma.202415981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Revised: 11/17/2024] [Indexed: 02/13/2025]
22
Ai L, Binek A, Zhemkov V, Cho JH, Haghani A, Kreimer S, Israely E, Arzt M, Chazarin B, Sundararaman N, Sharma A, Marbán E, Svendsen CN, Van Eyk JE. Single Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived from Human iPSCs and Adult Hearts. Mol Cell Proteomics 2025:100910. [PMID: 39855627 DOI: 10.1016/j.mcpro.2025.100910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 01/08/2025] [Accepted: 01/20/2025] [Indexed: 01/27/2025]  Open
23
Gong Y, Dai Y, Wu Q, Guo L, Yao X, Yang Q. Benchmark of Data Integration in Single-Cell Proteomics. Anal Chem 2025;97:1254-1263. [PMID: 39761355 DOI: 10.1021/acs.analchem.4c04933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
24
Zhao Q, Li S, Krall L, Li Q, Sun R, Yin Y, Fu J, Zhang X, Wang Y, Yang M. Deciphering cellular complexity: advances and future directions in single-cell protein analysis. Front Bioeng Biotechnol 2025;12:1507460. [PMID: 39877263 PMCID: PMC11772399 DOI: 10.3389/fbioe.2024.1507460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Accepted: 12/19/2024] [Indexed: 01/31/2025]  Open
25
Ryu T, Kim K, Asiimwe N, Na CH. Proteomic Insight Into Alzheimer's Disease Pathogenesis Pathways. Proteomics 2025:e202400298. [PMID: 39791267 DOI: 10.1002/pmic.202400298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Revised: 12/21/2024] [Accepted: 12/23/2024] [Indexed: 01/12/2025]
26
Calarco JA, Taylor SR, Miller DM. Detecting gene expression in Caenorhabditis elegans. Genetics 2025;229:1-108. [PMID: 39693264 PMCID: PMC11979774 DOI: 10.1093/genetics/iyae167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 09/30/2024] [Indexed: 12/20/2024]  Open
27
Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2025;68:5-102. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
28
Su PR, Chien MP. Functional Single-Cell Proteomics: Technology and Biological Applications. Methods Mol Biol 2025;2902:145-159. [PMID: 40029601 DOI: 10.1007/978-1-0716-4402-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
29
Nalla LV, Kanukolanu A, Yeduvaka M, Gajula SNR. Advancements in Single-Cell Proteomics and Mass Spectrometry-Based Techniques for Unmasking Cellular Diversity in Triple Negative Breast Cancer. Proteomics Clin Appl 2025;19:e202400101. [PMID: 39568435 PMCID: PMC11726282 DOI: 10.1002/prca.202400101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Revised: 11/04/2024] [Accepted: 11/08/2024] [Indexed: 11/22/2024]
30
Capelletti MM, Montini O, Ruini E, Tettamanti S, Savino AM, Sarno J. Unlocking the Heterogeneity in Acute Leukaemia: Dissection of Clonal Architecture and Metabolic Properties for Clinical Interventions. Int J Mol Sci 2024;26:45. [PMID: 39795903 PMCID: PMC11719665 DOI: 10.3390/ijms26010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Revised: 12/17/2024] [Accepted: 12/19/2024] [Indexed: 01/13/2025]  Open
31
Leduc A, Khoury L, Cantlon J, Khan S, Slavov N. Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP. Nat Protoc 2024;19:3750-3776. [PMID: 39117766 PMCID: PMC11614709 DOI: 10.1038/s41596-024-01033-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/27/2024] [Indexed: 08/10/2024]
32
Montes C, Zhang J, Nolan TM, Walley JW. Single-cell proteomics differentiates Arabidopsis root cell types. THE NEW PHYTOLOGIST 2024;244:1750-1759. [PMID: 38923440 DOI: 10.1111/nph.19923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024]
33
Yang D, Fang Y, Liu X, Ma J, Xu J, Dong H, Ding H, Wang D, Liu Q, Zhang F. Lensless On-Chip Chemiluminescence Imaging for High-Throughput Single-Cell Heterogeneity Analysis. NANO LETTERS 2024;24:14875-14883. [PMID: 39512117 DOI: 10.1021/acs.nanolett.4c04487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2024]
34
Qian L, Sun R, Aebersold R, Bühlmann P, Sander C, Guo T. AI-empowered perturbation proteomics for complex biological systems. CELL GENOMICS 2024;4:100691. [PMID: 39488205 PMCID: PMC11605689 DOI: 10.1016/j.xgen.2024.100691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 09/02/2024] [Accepted: 10/06/2024] [Indexed: 11/04/2024]
35
Yang L, Kim J, Chen L, Wei W, Wang J. Detection of >400 Cluster of Differentiation Biomarkers and Pathway Proteins in Single Immune Cells by Cyclic Multiplex In Situ Tagging for Single-Cell Proteomic Studies. Anal Chem 2024;96:17387-17395. [PMID: 39422499 PMCID: PMC11648578 DOI: 10.1021/acs.analchem.4c04239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
36
Senavirathna L, Ma C, Duong VA, Tsai HY, Chen R, Pan S. SLB-msSIM: a spectral library-based multiplex segmented SIM platform for single-cell proteomic analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.22.618936. [PMID: 39484511 PMCID: PMC11526955 DOI: 10.1101/2024.10.22.618936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2024]
37
Crouigneau R, Li YF, Auxillos J, Goncalves-Alves E, Marie R, Sandelin A, Pedersen SF. Mimicking and analyzing the tumor microenvironment. CELL REPORTS METHODS 2024;4:100866. [PMID: 39353424 PMCID: PMC11573787 DOI: 10.1016/j.crmeth.2024.100866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 07/22/2024] [Accepted: 09/09/2024] [Indexed: 10/04/2024]
38
Wang Z, Liu PK, Li L. A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics. ACS MEASUREMENT SCIENCE AU 2024;4:315-337. [PMID: 39184361 PMCID: PMC11342459 DOI: 10.1021/acsmeasuresciau.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 08/27/2024]
39
Stanisheuski S, Ebrahimi A, Vaidya KA, Jang HS, Yang L, Eddins AJ, Marean-Reardon C, Franco MC, Maier CS. Thermal inkjet makes label-free single-cell proteomics accessible and easy. Front Chem 2024;12:1428547. [PMID: 39233922 PMCID: PMC11371764 DOI: 10.3389/fchem.2024.1428547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 07/31/2024] [Indexed: 09/06/2024]  Open
40
Veličković M, Fillmore TL, Attah IK, Posso C, Pino JC, Zhao R, Williams SM, Veličković D, Jacobs JM, Burnum-Johnson KE, Zhu Y, Piehowski PD. Coupling Microdroplet-Based Sample Preparation, Multiplexed Isobaric Labeling, and Nanoflow Peptide Fractionation for Deep Proteome Profiling of the Tissue Microenvironment. Anal Chem 2024;96:12973-12982. [PMID: 39089681 PMCID: PMC11325296 DOI: 10.1021/acs.analchem.4c00523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/09/2024] [Accepted: 05/16/2024] [Indexed: 08/04/2024]
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Cutler R, Corveleyn L, Ctortecka C, Cantlon J, Jacome Vaca SA, Deforce D, Vijg J, Dhaenens M, Papanastasiou M, Carr SA, Sidoli S. Mass Spectrometry-based Profiling of Single-cell Histone Post-translational Modifications to Dissect Chromatin Heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602213. [PMID: 39211145 PMCID: PMC11361047 DOI: 10.1101/2024.07.05.602213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
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Gao Y, Shonai D, Trn M, Zhao J, Soderblom EJ, Garcia-Moreno SA, Gersbach CA, Wetsel WC, Dawson G, Velmeshev D, Jiang YH, Sloofman LG, Buxbaum JD, Soderling SH. Proximity analysis of native proteomes reveals phenotypic modifiers in a mouse model of autism and related neurodevelopmental conditions. Nat Commun 2024;15:6801. [PMID: 39122707 PMCID: PMC11316102 DOI: 10.1038/s41467-024-51037-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024]  Open
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Mun DG, Bhat FA, Joshi N, Sandoval L, Ding H, Jain A, Peterson JA, Kang T, Pujari GP, Tomlinson JL, Budhraja R, Zenka RM, Kannan N, Kipp BR, Dasari S, Gaspar-Maia A, Smoot RL, Kandasamy RK, Pandey A. Diversity of post-translational modifications and cell signaling revealed by single cell and single organelle mass spectrometry. Commun Biol 2024;7:884. [PMID: 39030393 PMCID: PMC11271535 DOI: 10.1038/s42003-024-06579-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]  Open
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Ctortecka C, Clark NM, Boyle BW, Seth A, Mani DR, Udeshi ND, Carr SA. Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications. Nat Commun 2024;15:5707. [PMID: 38977691 PMCID: PMC11231172 DOI: 10.1038/s41467-024-49651-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/14/2024] [Indexed: 07/10/2024]  Open
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Weng L, Yan G, Liu W, Tai Q, Gao M, Zhang X. Picoliter Single-Cell Reactor for Proteome Profiling by In Situ Cell Lysis, Protein Immobilization, Digestion, and Droplet Transfer. J Proteome Res 2024;23:2441-2451. [PMID: 38833655 DOI: 10.1021/acs.jproteome.4c00117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
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Xie X, Truong T, Huang S, Johnston SM, Hovanski S, Robinson A, Webber KGI, Lin HJL, Mun DG, Pandey A, Kelly RT. Multicolumn Nanoflow Liquid Chromatography with Accelerated Offline Gradient Generation for Robust and Sensitive Single-Cell Proteome Profiling. Anal Chem 2024;96:10534-10542. [PMID: 38915247 PMCID: PMC11482043 DOI: 10.1021/acs.analchem.4c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
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Ertürk A. Deep 3D histology powered by tissue clearing, omics and AI. Nat Methods 2024;21:1153-1165. [PMID: 38997593 DOI: 10.1038/s41592-024-02327-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 05/28/2024] [Indexed: 07/14/2024]
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Webel H, Niu L, Nielsen AB, Locard-Paulet M, Mann M, Jensen LJ, Rasmussen S. Imputation of label-free quantitative mass spectrometry-based proteomics data using self-supervised deep learning. Nat Commun 2024;15:5405. [PMID: 38926340 PMCID: PMC11208500 DOI: 10.1038/s41467-024-48711-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/13/2024] [Indexed: 06/28/2024]  Open
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Orsburn BC. Single cell proteomics by mass spectrometry reveals deep epigenetic insight into the actions of an orphan histone deacetylase inhibitor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574437. [PMID: 38260471 PMCID: PMC10802306 DOI: 10.1101/2024.01.05.574437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
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Rivero-Garcia I, Torres M, Sánchez-Cabo F. Deep generative models in single-cell omics. Comput Biol Med 2024;176:108561. [PMID: 38749321 DOI: 10.1016/j.compbiomed.2024.108561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/31/2024]
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