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For: Coscia F, Doll S, Bech JM, Schweizer L, Mund A, Lengyel E, Lindebjerg J, Madsen GI, Moreira JM, Mann M. A streamlined mass spectrometry-based proteomics workflow for large-scale FFPE tissue analysis. J Pathol 2020;251:100-112. [PMID: 32154592 DOI: 10.1002/path.5420] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 12/15/2022]
Number Cited by Other Article(s)
1
Najjar FN, Williamson YM, Cooper HC, Barr JR, Williams TL. Optimization of Extraction Methods for the Quantification of Proteins in Mammalian Tissues. Anal Chem 2025;97:10173-10179. [PMID: 40338194 DOI: 10.1021/acs.analchem.4c05751] [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: 05/09/2025]
2
Ryu T, Kim S, Thuraisamy T, Shin J, Jang Y, Kam T, Na CH. In-Depth Cell-Type-Specific Proteome Landscape of the Brain from Human Amyloid-β Overexpression Mouse Model. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025;12:e2409318. [PMID: 40345165 PMCID: PMC12120748 DOI: 10.1002/advs.202409318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 04/18/2025] [Indexed: 05/11/2025]
3
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]
4
Rosenberger FA, Mädler SC, Thorhauge KH, Steigerwald S, Fromme M, Lebedev M, Weiss CAM, Oeller M, Wahle M, Metousis A, Zwiebel M, Schmacke NA, Detlefsen S, Boor P, Fabián O, Fraňková S, Krag A, Strnad P, Mann M. Deep Visual Proteomics maps proteotoxicity in a genetic liver disease. Nature 2025:10.1038/s41586-025-08885-4. [PMID: 40240610 DOI: 10.1038/s41586-025-08885-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Accepted: 03/11/2025] [Indexed: 04/18/2025]
5
Ji S, Cao L, Gao J, Du Y, Ye Z, Lou X, Liu F, Zhang Y, Xu J, Shi X, Wang H, Li P, Li Y, Chen H, Yang Z, Gao S, Zhang W, Huang D, Ni S, Wei M, Wang F, Wang Y, Ding T, Jing D, Fan G, Gong Z, Lu R, Qin Y, Chen J, Xu X, Wang P, Zhang B, Ding L, Robles AI, Rodriguez H, Chang DK, Hruban RH, Gao D, Gao D, Jin G, Zhou H, Wu J, Yu X. Proteogenomic characterization of non-functional pancreatic neuroendocrine tumors unravels clinically relevant subgroups. Cancer Cell 2025;43:776-796.e14. [PMID: 40185092 DOI: 10.1016/j.ccell.2025.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 01/27/2025] [Accepted: 03/12/2025] [Indexed: 04/07/2025]
6
Johansen A, Sandve GKF, Maxwell JR, Smithson G, Sollid LM, Stamnaes J. Biopsy Proteome Score Performs Well as an Effect Measure in a Gluten Challenge Trial of Celiac Disease. Clin Gastroenterol Hepatol 2025;23:758-765.e8. [PMID: 39209203 DOI: 10.1016/j.cgh.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/22/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
7
Ha A, Woolman M, Waas M, Govindarajan M, Kislinger T. Recent implementations of data-independent acquisition for cancer biomarker discovery in biological fluids. Expert Rev Proteomics 2025;22:163-176. [PMID: 40227112 DOI: 10.1080/14789450.2025.2491355] [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: 01/29/2025] [Revised: 03/26/2025] [Accepted: 04/06/2025] [Indexed: 04/15/2025]
8
Zhang J, Wang Y, Liu Y, Chen H, Chai N, Zhao Y, Li Y, Li X, He J, Zhang H. Proteomic profiling reveals biological processes and biomarkers involved in the pathogenesis of occult breast cancer. BMC Cancer 2025;25:231. [PMID: 39930421 PMCID: PMC11812265 DOI: 10.1186/s12885-025-13657-4] [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: 10/13/2024] [Accepted: 02/05/2025] [Indexed: 02/13/2025]  Open
9
Koh JMS, Sykes EK, Rukhaya J, Anees A, Zhong Q, Jackson C, Panizza BJ, Reddel RR, Balleine RL, Hains PG, Robinson PJ. The effect of storage time and temperature on the proteomic analysis of FFPE tissue sections. Clin Proteomics 2025;22:5. [PMID: 39910438 DOI: 10.1186/s12014-025-09529-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 01/22/2025] [Indexed: 02/07/2025]  Open
10
Chatterjee S, Zaia J, Sethi MK. Mass Spectrometry-Based Glycomics and Proteomics Profiling of On-Slide Digested Tissue from Complex Biological Samples. Methods Mol Biol 2025;2884:279-303. [PMID: 39716010 DOI: 10.1007/978-1-0716-4298-6_18] [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: 12/25/2024]
11
Tüshaus J, Eckert S, Schliemann M, Zhou Y, Pfeiffer P, Halves C, Fusco F, Weigel J, Hönikl L, Butenschön V, Todorova R, Rauert-Wunderlich H, The M, Rosenwald A, Heinemann V, Holch J, Steiger K, Delbridge C, Meyer B, Weichert W, Mogler C, Kuhn PH, Kuster B. Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study. EMBO J 2025;44:304-329. [PMID: 39558110 PMCID: PMC11697351 DOI: 10.1038/s44318-024-00289-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: 06/19/2024] [Revised: 10/08/2024] [Accepted: 10/14/2024] [Indexed: 11/20/2024]  Open
12
Isaiah AR, Luies L, Loots DT, Williams AA, Vlok M, Chegou NN, Tutu van Furth M, van der Kuip M, Mason S. Protocol for unified metabolomics and proteomics analysis of formalin-fixed paraffin-embedded tissue. STAR Protoc 2024;5:103442. [PMID: 39522166 PMCID: PMC11585672 DOI: 10.1016/j.xpro.2024.103442] [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: 07/04/2024] [Revised: 08/23/2024] [Accepted: 10/16/2024] [Indexed: 11/16/2024]  Open
13
Haines M, Thorup JR, Gohsman S, Ctortecka C, Newton C, Rohrer DC, Hostetter G, Mani DR, Gillette MA, Satpathy S, Carr SA. High-throughput proteomic and phosphoproteomic analysis of formalin-fixed paraffin-embedded tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.17.624038. [PMID: 39605438 PMCID: PMC11601474 DOI: 10.1101/2024.11.17.624038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
14
Nordmann TM, Mund A, Mann M. A new understanding of tissue biology from MS-based proteomics at single-cell resolution. Nat Methods 2024;21:2220-2222. [PMID: 39643675 DOI: 10.1038/s41592-024-02541-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2024]
15
Xu Y, Wang X, Li Y, Mao Y, Su Y, Mao Y, Yang Y, Gao W, Fu C, Chen W, Ye X, Liang F, Bai P, Sun Y, Li S, Xu R, Tian R. Multimodal single cell-resolved spatial proteomics reveal pancreatic tumor heterogeneity. Nat Commun 2024;15:10100. [PMID: 39572534 PMCID: PMC11582669 DOI: 10.1038/s41467-024-54438-0] [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: 10/20/2023] [Accepted: 11/12/2024] [Indexed: 11/24/2024]  Open
16
Gronauer TF, Eck LK, Ludwig C, Sieber SA. A Photocrosslinking Probe to Capture the Substrates of Caseinolytic Protease P. Angew Chem Int Ed Engl 2024;63:e202409220. [PMID: 39073273 DOI: 10.1002/anie.202409220] [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: 05/15/2024] [Revised: 07/17/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
17
Egbejiogu BC, Donnarumma F, Murray KK. Infrared Laser Ablation and Capture of Formalin-Fixed Paraffin-Embedded Tissue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39494617 DOI: 10.1021/jasms.4c00299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2024]
18
Schwab SK, Harris PS, Michel C, McGinnis CD, Nahomi RB, Assiri MA, Reisdorph R, Henriksen K, Orlicky DJ, Levi M, Rosenberg A, Nagaraj RH, Fritz KS. Quantifying Protein Acetylation in Diabetic Nephropathy from Formalin-Fixed Paraffin-Embedded Tissue. Proteomics Clin Appl 2024;18:e202400018. [PMID: 38923810 DOI: 10.1002/prca.202400018] [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: 02/29/2024] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024]
19
Montero-Calle A, Garranzo-Asensio M, Poves C, Sanz R, Dziakova J, Peláez-García A, de Los Ríos V, Martinez-Useros J, Fernández-Aceñero MJ, Barderas R. In-Depth Proteomic Analysis of Paraffin-Embedded Tissue Samples from Colorectal Cancer Patients Revealed TXNDC17 and SLC8A1 as Key Proteins Associated with the Disease. J Proteome Res 2024;23:4802-4820. [PMID: 39441737 DOI: 10.1021/acs.jproteome.3c00749] [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: 10/25/2024]
20
Zhang T, Li Y, Pan L, Sha J, Bailey M, Faure-Kumar E, Williams CK, Wohlschlegel J, Magaki S, Niu C, Lee Y, Su YC, Li X, Vinters HV, Geschwind DH. Brain-wide alterations revealed by spatial transcriptomics and proteomics in COVID-19 infection. NATURE AGING 2024;4:1598-1618. [PMID: 39543407 PMCID: PMC11867587 DOI: 10.1038/s43587-024-00730-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 09/25/2024] [Indexed: 11/17/2024]
21
Shao X, Huang Y, Xu R, He Q, Zhang M, He F, Wang D. ZASP: A Highly Compatible and Sensitive ZnCl2 Precipitation-Assisted Sample Preparation Method for Proteomic Analysis. Mol Cell Proteomics 2024;23:100837. [PMID: 39243857 PMCID: PMC11492125 DOI: 10.1016/j.mcpro.2024.100837] [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: 12/11/2023] [Revised: 08/30/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]  Open
22
Ludwig ML, Moline D, Horrmann A, Boytim E, Larson G, Arafa AT, Sayeda M, Lozada JR, Bergom HE, Day A, Dasaraju S, Dehm SM, Murugan P, Hwang J, Drake JM, Antonarakis ES. Integrated multi-omics assessment of lineage plasticity in a prostate cancer patient with brain and dural metastases. NPJ Precis Oncol 2024;8:215. [PMID: 39349591 PMCID: PMC11443004 DOI: 10.1038/s41698-024-00713-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024]  Open
23
Kabatnik S, Post F, Drici L, Bartels AS, Strauss MT, Zheng X, Madsen GI, Mund A, Rosenberger FA, Moreira J, Mann M. Spatial characterization and stratification of colorectal adenomas by deep visual proteomics. iScience 2024;27:110620. [PMID: 39252972 PMCID: PMC11381895 DOI: 10.1016/j.isci.2024.110620] [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: 12/22/2023] [Revised: 05/13/2024] [Accepted: 07/26/2024] [Indexed: 09/11/2024]  Open
24
Harder BJ, Lekkerkerker AN, Casavant EP, Hackney JA, Nguyen A, McBride JM, Mathews WR, Anania VG. Comprehensive profiling of the human fecal proteome from IBD patients with DIA-MS enables evaluation of disease-relevant proteins. Proteomics Clin Appl 2024;18:e2300075. [PMID: 38552248 DOI: 10.1002/prca.202300075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 02/26/2024] [Accepted: 03/08/2024] [Indexed: 11/18/2024]
25
Humphries EM, Loudon C, Craft GE, Hains PG, Robinson PJ. Quantitative Comparison of Deparaffinization, Rehydration, and Extraction Methods for FFPE Tissue Proteomics and Phosphoproteomics. Anal Chem 2024;96:13358-13370. [PMID: 39102789 DOI: 10.1021/acs.analchem.3c04479] [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: 08/07/2024]
26
Rosin NL, Winstone TML, Kelley M, Biernaskie J, Dufour A, Orton DJ. Targeted proteomic approach for quantification of collagen type I and type III in formalin-fixed paraffin-embedded tissue. Sci Rep 2024;14:17769. [PMID: 39090134 PMCID: PMC11294326 DOI: 10.1038/s41598-024-68377-9] [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: 03/05/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024]  Open
27
Johansen A, Sandve GKF, Ibsen JH, Lundin KEA, Sollid LM, Stamnaes J. Biopsy Proteome Scoring to Determine Mucosal Remodeling in Celiac Disease. Gastroenterology 2024;167:493-504.e10. [PMID: 38467384 DOI: 10.1053/j.gastro.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/14/2024] [Accepted: 03/05/2024] [Indexed: 03/13/2024]
28
Doll S, Schweizer L, Bollwein C, Steiger K, Pfarr N, Walker M, Wörtler K, Knebel C, von Eisenhart-Rothe R, Hartmann W, Weichert W, Mann M, Kuhn PH, Specht K. Proteomic Characterization of Undifferentiated Small Round Cell Sarcomas With EWSR1 and CIC::DUX4 Translocations Reveals Diverging Tumor Biology and Distinct Diagnostic Markers. Mod Pathol 2024;37:100511. [PMID: 38705279 DOI: 10.1016/j.modpat.2024.100511] [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: 10/16/2023] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/07/2024]
29
Sun BB, Suhre K, Gibson BW. Promises and Challenges of populational Proteomics in Health and Disease. Mol Cell Proteomics 2024;23:100786. [PMID: 38761890 PMCID: PMC11193116 DOI: 10.1016/j.mcpro.2024.100786] [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: 02/06/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024]  Open
30
Naimy S, Sølberg JBK, Kuczek DE, Løvendorf MB, Bzorek M, Litman T, Mund A, Rahbek Gjerdrum LM, Clark RA, Mann M, Dyring-Andersen B. Comparative Quantitative Proteomic Analysis of Melanoma Subtypes, Nevus-Associated Melanoma, and Corresponding Nevi. J Invest Dermatol 2024;144:1608-1621.e4. [PMID: 38185415 DOI: 10.1016/j.jid.2023.12.011] [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: 07/04/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024]
31
Faktor J, Kote S, Bienkowski M, Hupp TR, Marek-Trzonkowska N. Novel FFPE proteomics method suggests prolactin induced protein as hormone induced cytoskeleton remodeling spatial biomarker. Commun Biol 2024;7:708. [PMID: 38851810 PMCID: PMC11162451 DOI: 10.1038/s42003-024-06354-8] [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: 01/20/2023] [Accepted: 05/20/2024] [Indexed: 06/10/2024]  Open
32
Pruszkowska-Przybylska P, Dupont ME, Jacobsen SB, Smerup M, Tfelt-Hansen J, Morling N, Andersen JD. Evaluation of DNAmAge in paired fresh, frozen, and formalin-fixed paraffin-embedded heart tissues. PLoS One 2024;19:e0299557. [PMID: 38718072 PMCID: PMC11078437 DOI: 10.1371/journal.pone.0299557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/12/2024] [Indexed: 05/12/2024]  Open
33
Topitsch A, Halstenbach T, Rothweiler R, Fretwurst T, Nelson K, Schilling O. Mass Spectrometry-Based Proteomics of Poly(methylmethacrylate)-Embedded Bone. J Proteome Res 2024;23:1810-1820. [PMID: 38634750 DOI: 10.1021/acs.jproteome.4c00046] [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: 04/19/2024]
34
Makhmut A, Qin D, Hartlmayr D, Seth A, Coscia F. An Automated and Fast Sample Preparation Workflow for Laser Microdissection Guided Ultrasensitive Proteomics. Mol Cell Proteomics 2024;23:100750. [PMID: 38513891 PMCID: PMC11067455 DOI: 10.1016/j.mcpro.2024.100750] [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: 12/08/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]  Open
35
Xavier D, Lucas N, Williams SG, Koh JMS, Ashman K, Loudon C, Reddel R, Hains PG, Robinson PJ. Heat 'n Beat: A Universal High-Throughput End-to-End Proteomics Sample Processing Platform in under an Hour. Anal Chem 2024;96:4093-4102. [PMID: 38427620 DOI: 10.1021/acs.analchem.3c04708] [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: 03/03/2024]
36
Dokanei S, Minai‐Tehrani D, Moghoofei M, Rostamian M. Investigating the relationship between Epstein-Barr virus infection and gastric cancer: A systematic review and meta-analysis. Health Sci Rep 2024;7:e1976. [PMID: 38505684 PMCID: PMC10948593 DOI: 10.1002/hsr2.1976] [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: 08/26/2023] [Revised: 02/06/2024] [Accepted: 02/28/2024] [Indexed: 03/21/2024]  Open
37
Patton A, Dermawan JK. Current updates in sarcoma biomarker discovery: emphasis on next-generation sequencing-based methods. Pathology 2024;56:274-282. [PMID: 38185613 DOI: 10.1016/j.pathol.2023.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/25/2023] [Accepted: 10/29/2023] [Indexed: 01/09/2024]
38
Dieters-Castator DZ, Manzanillo P, Yang HY, Modak RV, Rardin MJ, Gibson BW. Magnetic Bead-Based Workflow for Sensitive and Streamlined Cell Surface Proteomics. J Proteome Res 2024;23:618-632. [PMID: 38226771 DOI: 10.1021/acs.jproteome.3c00432] [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: 01/17/2024]
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G Jagadeeshaprasad M, Zeng J, Zheng N. LC-MS bioanalysis of protein biomarkers and protein therapeutics in formalin-fixed paraffin-embedded tissue specimens. Bioanalysis 2024;16:245-258. [PMID: 38226835 DOI: 10.4155/bio-2023-0210] [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: 01/17/2024]  Open
40
Yan HJ, Lin SC, Xu SH, Gao YB, Zhou BJ, Zhou R, Chen FM, Li FR. Proteomic analysis reveals LRPAP1 as a key player in the micropapillary pattern metastasis of lung adenocarcinoma. Heliyon 2024;10:e23913. [PMID: 38226250 PMCID: PMC10788494 DOI: 10.1016/j.heliyon.2023.e23913] [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: 08/04/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/17/2024]  Open
41
Thielert M, Weiss CAM, Mann M, Rosenberger FA. Spatial Proteomics of Single Hepatocytes with Multiplexed Data-Independent Acquisition (mDIA). Methods Mol Biol 2024;2817:97-113. [PMID: 38907150 DOI: 10.1007/978-1-0716-3934-4_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: 06/23/2024]
42
Wang YE, Zeng WL, Cao ST, Zou JP, Liu CT, Shi JM, Li J, Qiu F, Wang Y. Development of a sample preparation method for micro-proteomics analysis of the formaldehyde-fixed paraffin-embedded liver tissue samples. Talanta 2024;266:125106. [PMID: 37639870 DOI: 10.1016/j.talanta.2023.125106] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
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Darville LNF, Lockhart JH, Putty Reddy S, Fang B, Izumi V, Boyle TA, Haura EB, Flores ER, Koomen JM. A Fast-Tracking Sample Preparation Protocol for Proteomics of Formalin-Fixed Paraffin-Embedded Tumor Tissues. Methods Mol Biol 2024;2823:193-223. [PMID: 39052222 PMCID: PMC11648944 DOI: 10.1007/978-1-0716-3922-1_13] [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: 07/27/2024]
44
Mar D, Babenko IM, Zhang R, Noble WS, Denisenko O, Vaisar T, Bomsztyk K. A High-Throughput PIXUL-Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes. J Transl Med 2024;104:100282. [PMID: 37924947 PMCID: PMC10872585 DOI: 10.1016/j.labinv.2023.100282] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]  Open
45
Tüshaus J, Sakhteman A, Lechner S, The M, Mucha E, Krisp C, Schlegel J, Delbridge C, Kuster B. A region-resolved proteomic map of the human brain enabled by high-throughput proteomics. EMBO J 2023;42:e114665. [PMID: 37916885 PMCID: PMC10690467 DOI: 10.15252/embj.2023114665] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023]  Open
46
Brouwer NP, Webbink L, Haddad TS, Rutgers N, van Vliet S, Wood CS, Jansen PW, Lafarge MW, de Wilt JH, Hugen N, Simmer F, Jamieson NB, Tauriello DV, Kölzer VH, Vermeulen M, Nagtegaal ID. Transcriptomics and proteomics reveal distinct biology for lymph node metastases and tumour deposits in colorectal cancer. J Pathol 2023;261:401-412. [PMID: 37792663 DOI: 10.1002/path.6196] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/12/2023] [Accepted: 08/02/2023] [Indexed: 10/06/2023]
47
Cho A, Ahn J, Kim A, Lee JH, Ryu HS, Kim KM, Yi EC. Proteomics analysis of an individual formalin-fixed paraffin-embedded tissue section using isobaric-tag amplification. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023;37:e9616. [PMID: 37817342 DOI: 10.1002/rcm.9616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 10/12/2023]
48
Davis S, Scott C, Oetjen J, Charles PD, Kessler BM, Ansorge O, Fischer R. Deep topographic proteomics of a human brain tumour. Nat Commun 2023;14:7710. [PMID: 38001067 PMCID: PMC10673928 DOI: 10.1038/s41467-023-43520-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]  Open
49
Makhmut A, Qin D, Fritzsche S, Nimo J, König J, Coscia F. A framework for ultra-low-input spatial tissue proteomics. Cell Syst 2023;14:1002-1014.e5. [PMID: 37909047 DOI: 10.1016/j.cels.2023.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/03/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023]
50
Kitata RB, Yang JC, Chen YJ. Advances in data-independent acquisition mass spectrometry towards comprehensive digital proteome landscape. MASS SPECTROMETRY REVIEWS 2023;42:2324-2348. [PMID: 35645145 DOI: 10.1002/mas.21781] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 06/15/2023]
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