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For: Kirkwood KJ, Ahmad Y, Larance M, Lamond AI. Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics. Mol Cell Proteomics 2013;12:3851-73. [PMID: 24043423 PMCID: PMC3861729 DOI: 10.1074/mcp.m113.032367] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
Number Cited by Other Article(s)
1
Fischer SN, Claussen ER, Kourtis S, Sdelci S, Orchard S, Hermjakob H, Kustatscher G, Drew K. hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments. Mol Syst Biol 2025:10.1038/s44320-025-00121-5. [PMID: 40425816 DOI: 10.1038/s44320-025-00121-5] [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: 11/22/2024] [Revised: 05/07/2025] [Accepted: 05/09/2025] [Indexed: 05/29/2025]  Open
2
Doron-Mandel E, Bokor BJ, Ma Y, Street LA, Tang LC, Abdou AA, Shah NH, Rosenberger G, Jovanovic M. SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation. Nat Commun 2025;16:1176. [PMID: 39885126 PMCID: PMC11782603 DOI: 10.1038/s41467-025-56303-0] [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: 05/16/2024] [Accepted: 01/13/2025] [Indexed: 02/01/2025]  Open
3
Foo B, Amedei H, Kaur S, Jaawan S, Boshnakovska A, Gall T, de Boer RA, Silljé HHW, Urlaub H, Rehling P, Lenz C, Lehnart SE. Unbiased complexome profiling and global proteomics analysis reveals mitochondrial impairment and potential changes at the intercalated disk in presymptomatic R14Δ/+ mice hearts. PLoS One 2024;19:e0311203. [PMID: 39446877 PMCID: PMC11501035 DOI: 10.1371/journal.pone.0311203] [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: 05/24/2024] [Accepted: 09/15/2024] [Indexed: 10/26/2024]  Open
4
Fischer SN, Claussen ER, Kourtis S, Sdelci S, Orchard S, Hermjakob H, Kustatscher G, Drew K. hu.MAP3.0: Atlas of human protein complexes by integration of > 25,000 proteomic experiments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.11.617930. [PMID: 39464102 PMCID: PMC11507723 DOI: 10.1101/2024.10.11.617930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
5
Takagi S, Suzuki N, Ishihama Y. Revisiting Protein Reversed-Phase Chromatography for Bottom-Up Proteomics. J Proteome Res 2024;23:4704-4714. [PMID: 39293027 DOI: 10.1021/acs.jproteome.4c00642] [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: 09/20/2024]
6
Street LA, Rothamel KL, Brannan KW, Jin W, Bokor BJ, Dong K, Rhine K, Madrigal A, Al-Azzam N, Kim JK, Ma Y, Gorhe D, Abdou A, Wolin E, Mizrahi O, Ahdout J, Mujumdar M, Doron-Mandel E, Jovanovic M, Yeo GW. Large-scale map of RNA-binding protein interactomes across the mRNA life cycle. Mol Cell 2024;84:3790-3809.e8. [PMID: 39303721 PMCID: PMC11530141 DOI: 10.1016/j.molcel.2024.08.030] [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: 06/07/2023] [Revised: 04/18/2024] [Accepted: 08/26/2024] [Indexed: 09/22/2024]
7
Kim D, Nita-Lazar A. Progress in mass spectrometry approaches to profiling protein-protein interactions in the studies of the innate immune system. JOURNAL OF PROTEINS AND PROTEOMICS 2024;15:545-559. [PMID: 39380887 PMCID: PMC11460538 DOI: 10.1007/s42485-024-00156-6] [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: 03/31/2024] [Revised: 06/04/2024] [Accepted: 06/24/2024] [Indexed: 10/10/2024]
8
Larson J, Tokmina-Lukaszewska M, Payne D, Spietz RL, Fausset H, Alam MG, Brekke BK, Pauley J, Hasenoehrl EJ, Shepard EM, Boyd ES, Bothner B. Impact of mineral and non-mineral sources of iron and sulfur on the metalloproteome of Methanosarcina barkeri. Appl Environ Microbiol 2024;90:e0051624. [PMID: 39023267 PMCID: PMC11337800 DOI: 10.1128/aem.00516-24] [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: 03/21/2024] [Accepted: 06/27/2024] [Indexed: 07/20/2024]  Open
9
Doron-Mandel E, Bokor BJ, Ma Y, Street LA, Tang LC, Abdou AA, Shah NH, Rosenberger G, Jovanovic M. A Multiplexed SEC-MS Approach to Systematically Study the Interplay Between Protein Assembly-States and Phosphorylation Events. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.12.523793. [PMID: 36711903 PMCID: PMC9882152 DOI: 10.1101/2023.01.12.523793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
10
LIU W, WENG L, GAO M, ZHANG X. [Applications of high performance liquid chromatography-mass spectrometry in proteomics]. Se Pu 2024;42:601-612. [PMID: 38966969 PMCID: PMC11224944 DOI: 10.3724/sp.j.1123.2023.11006] [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: 11/09/2023] [Indexed: 07/06/2024]  Open
11
Holfeld A, Schuster D, Sesterhenn F, Gillingham AK, Stalder P, Haenseler W, Barrio-Hernandez I, Ghosh D, Vowles J, Cowley SA, Nagel L, Khanppnavar B, Serdiuk T, Beltrao P, Korkhov VM, Munro S, Riek R, de Souza N, Picotti P. Systematic identification of structure-specific protein-protein interactions. Mol Syst Biol 2024;20:651-675. [PMID: 38702390 PMCID: PMC11148107 DOI: 10.1038/s44320-024-00037-6] [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] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/06/2024]  Open
12
Ng CCA, Zhou Y, Yao ZP. Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review. Anal Chim Acta 2023;1268:341330. [PMID: 37268337 DOI: 10.1016/j.aca.2023.341330] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 06/04/2023]
13
Palukuri MV, Patil RS, Marcotte EM. Molecular complex detection in protein interaction networks through reinforcement learning. BMC Bioinformatics 2023;24:306. [PMID: 37532987 PMCID: PMC10394916 DOI: 10.1186/s12859-023-05425-7] [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: 02/05/2023] [Accepted: 07/20/2023] [Indexed: 08/04/2023]  Open
14
Street L, Rothamel K, Brannan K, Jin W, Bokor B, Dong K, Rhine K, Madrigal A, Al-Azzam N, Kim JK, Ma Y, Abdou A, Wolin E, Doron-Mandel E, Ahdout J, Mujumdar M, Jovanovic M, Yeo GW. Large-scale map of RNA binding protein interactomes across the mRNA life-cycle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544225. [PMID: 37333282 PMCID: PMC10274859 DOI: 10.1101/2023.06.08.544225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
15
Lazear MR, Remsberg JR, Jaeger MG, Rothamel K, Her HL, DeMeester KE, Njomen E, Hogg SJ, Rahman J, Whitby LR, Won SJ, Schafroth MA, Ogasawara D, Yokoyama M, Lindsey GL, Li H, Germain J, Barbas S, Vaughan J, Hanigan TW, Vartabedian VF, Reinhardt CJ, Dix MM, Koo SJ, Heo I, Teijaro JR, Simon GM, Ghosh B, Abdel-Wahab O, Ahn K, Saghatelian A, Melillo B, Schreiber SL, Yeo GW, Cravatt BF. Proteomic discovery of chemical probes that perturb protein complexes in human cells. Mol Cell 2023;83:1725-1742.e12. [PMID: 37084731 PMCID: PMC10198961 DOI: 10.1016/j.molcel.2023.03.026] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/09/2023] [Accepted: 03/28/2023] [Indexed: 04/23/2023]
16
High-Throughput Proteome Profiling of Plasma and Native Plasma Complexes Using Native Chromatography. Methods Mol Biol 2023;2628:53-79. [PMID: 36781779 DOI: 10.1007/978-1-0716-2978-9_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
17
Samant RS, Batista S, Larance M, Ozer B, Milton CI, Bludau I, Wu E, Biggins L, Andrews S, Hervieu A, Johnston HE, Al-Lazikhani B, Lamond AI, Clarke PA, Workman P. Native Size-Exclusion Chromatography-Based Mass Spectrometry Reveals New Components of the Early Heat Shock Protein 90 Inhibition Response Among Limited Global Changes. Mol Cell Proteomics 2023;22:100485. [PMID: 36549590 PMCID: PMC9898794 DOI: 10.1016/j.mcpro.2022.100485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/16/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]  Open
18
Peter C, Schulz WA, Whongsiri P. Characterization of Native COMPASS Complex in Urothelial Carcinoma Cells by Size Exclusion Chromatography. Methods Mol Biol 2023;2684:101-109. [PMID: 37410229 DOI: 10.1007/978-1-0716-3291-8_5] [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: 07/07/2023]
19
Chihara K, Gerovac M, Hör J, Vogel J. Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq). RNA (NEW YORK, N.Y.) 2022;29:rna.079439.122. [PMID: 36328526 PMCID: PMC9808575 DOI: 10.1261/rna.079439.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
20
Zhang Y, Yang L, Fang K, Li Q, Xu H, Ren Y, Zi J, Chen CD, Liu S. Dynamic Responses of Chromosome-Binding Protein Complexes to Meiotic Prophase I of Mouse Spermatocyte. J Proteome Res 2022;21:2715-2726. [PMID: 36223561 DOI: 10.1021/acs.jproteome.2c00414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
21
Pauwels J, Fijałkowska D, Eyckerman S, Gevaert K. Mass spectrometry and the cellular surfaceome. MASS SPECTROMETRY REVIEWS 2022;41:804-841. [PMID: 33655572 DOI: 10.1002/mas.21690] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
22
Global landscape of protein complexes in postprandial-state livers from diet-induced obese and lean mice. Biochem Biophys Res Commun 2022;629:40-46. [DOI: 10.1016/j.bbrc.2022.08.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022]
23
Xu C, Wang B, Yang L, Zhongming Hu L, Yi L, Wang Y, Chen S, Emili A, Wan C. Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022;20:715-727. [PMID: 33636367 PMCID: PMC9880817 DOI: 10.1016/j.gpb.2020.06.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 04/04/2020] [Accepted: 06/12/2020] [Indexed: 01/31/2023]
24
Rogawski R, Sharon M. Characterizing Endogenous Protein Complexes with Biological Mass Spectrometry. Chem Rev 2022;122:7386-7414. [PMID: 34406752 PMCID: PMC9052418 DOI: 10.1021/acs.chemrev.1c00217] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Indexed: 01/11/2023]
25
Xu C, Wang B, Heng H, Huang J, Wan C. Comparative Network Biology Discovers Protein Complexes That Underline Cellular Differentiation in Anabaena sp. Mol Cell Proteomics 2022;21:100224. [PMID: 35288331 PMCID: PMC9035410 DOI: 10.1016/j.mcpro.2022.100224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 02/20/2022] [Accepted: 03/10/2022] [Indexed: 01/11/2023]  Open
26
Schessner JP, Voytik E, Bludau I. A practical guide to interpreting and generating bottom-up proteomics data visualizations. Proteomics 2022;22:e2100103. [PMID: 35107884 DOI: 10.1002/pmic.202100103] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/22/2021] [Accepted: 01/20/2022] [Indexed: 11/10/2022]
27
Xiong E, Cao D, Qu C, Zhao P, Wu Z, Yin D, Zhao Q, Gong F. Multilocation proteins in organelle communication: Based on protein-protein interactions. PLANT DIRECT 2022;6:e386. [PMID: 35229068 PMCID: PMC8861329 DOI: 10.1002/pld3.386] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 12/17/2021] [Accepted: 01/18/2022] [Indexed: 05/25/2023]
28
Laulumaa S, Varjosalo M. Commander Complex-A Multifaceted Operator in Intracellular Signaling and Cargo. Cells 2021;10:cells10123447. [PMID: 34943955 PMCID: PMC8700231 DOI: 10.3390/cells10123447] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022]  Open
29
Landeira-Viñuela A, Díez P, Juanes-Velasco P, Lécrevisse Q, Orfao A, De Las Rivas J, Fuentes M. Deepening into Intracellular Signaling Landscape through Integrative Spatial Proteomics and Transcriptomics in a Lymphoma Model. Biomolecules 2021;11:1776. [PMID: 34944421 PMCID: PMC8699084 DOI: 10.3390/biom11121776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/23/2021] [Indexed: 12/12/2022]  Open
30
Chirițoiu GN, Chirițoiu M, Munteanu CV. Dataset of human EDEM2 melanoma cells proteomics, affinity proteomics and deglycoproteomics. Data Brief 2021;39:107471. [PMID: 34712749 PMCID: PMC8529096 DOI: 10.1016/j.dib.2021.107471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/02/2021] [Accepted: 10/04/2021] [Indexed: 11/19/2022]  Open
31
Munson MJ, Mathai BJ, Ng MYW, Trachsel-Moncho L, de la Ballina LR, Schultz SW, Aman Y, Lystad AH, Singh S, Singh S, Wesche J, Fang EF, Simonsen A. GAK and PRKCD are positive regulators of PRKN-independent mitophagy. Nat Commun 2021;12:6101. [PMID: 34671015 DOI: 10.1101/2020.11.05.369496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 09/29/2021] [Indexed: 05/28/2023]  Open
32
Munson MJ, Mathai BJ, Ng MYW, Trachsel-Moncho L, de la Ballina LR, Schultz SW, Aman Y, Lystad AH, Singh S, Singh S, Wesche J, Fang EF, Simonsen A. GAK and PRKCD are positive regulators of PRKN-independent mitophagy. Nat Commun 2021;12:6101. [PMID: 34671015 PMCID: PMC8528926 DOI: 10.1038/s41467-021-26331-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 09/29/2021] [Indexed: 12/26/2022]  Open
33
Using yeast two-hybrid system and molecular dynamics simulation to detect venom protein-protein interactions. Curr Res Toxicol 2021;2:93-98. [PMID: 34345854 PMCID: PMC8320608 DOI: 10.1016/j.crtox.2021.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/14/2021] [Accepted: 02/19/2021] [Indexed: 12/13/2022]  Open
34
Munteanu CVA, Chirițoiu GN, Chirițoiu M, Ghenea S, Petrescu AJ, Petrescu ȘM. Affinity proteomics and deglycoproteomics uncover novel EDEM2 endogenous substrates and an integrative ERAD network. Mol Cell Proteomics 2021;20:100125. [PMID: 34332121 PMCID: PMC8455867 DOI: 10.1016/j.mcpro.2021.100125] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 07/09/2021] [Accepted: 07/25/2021] [Indexed: 02/08/2023]  Open
35
Hu Y, Park N, Seo KS, Park JY, Somarathne RP, Olivier AK, Fitzkee NC, Thornton JA. Pneumococcal surface adhesion A protein (PsaA) interacts with human Annexin A2 on airway epithelial cells. Virulence 2021;12:1841-1854. [PMID: 34233589 PMCID: PMC8274441 DOI: 10.1080/21505594.2021.1947176] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]  Open
36
Drew K, Wallingford JB, Marcotte EM. hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies. Mol Syst Biol 2021;17:e10016. [PMID: 33973408 PMCID: PMC8111494 DOI: 10.15252/msb.202010016] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/30/2022]  Open
37
PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. Nat Methods 2021;18:520-527. [PMID: 33859439 DOI: 10.1038/s41592-021-01107-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 03/03/2021] [Indexed: 02/02/2023]
38
Bludau I. Discovery-Versus Hypothesis-Driven Detection of Protein-Protein Interactions and Complexes. Int J Mol Sci 2021;22:4450. [PMID: 33923221 PMCID: PMC8123138 DOI: 10.3390/ijms22094450] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/13/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022]  Open
39
Gerovac M, Vogel J, Smirnov A. The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches. Front Mol Biosci 2021;8:661448. [PMID: 33898526 PMCID: PMC8058203 DOI: 10.3389/fmolb.2021.661448] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022]  Open
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Lee Y, Szymanski DB. Multimerization variants as potential drivers of neofunctionalization. SCIENCE ADVANCES 2021;7:eabf0984. [PMID: 33771868 PMCID: PMC7997512 DOI: 10.1126/sciadv.abf0984] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/29/2021] [Indexed: 05/05/2023]
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Klann K, Tascher G, Münch C. Virus systems biology: Proteomics profiling of dynamic protein networks during infection. Adv Virus Res 2021;109:1-29. [PMID: 33934824 DOI: 10.1016/bs.aivir.2020.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Lee J, Oh S, Bhattacharya S, Zhang Y, Florens L, Washburn MP, Workman JL. The plasticity of the pyruvate dehydrogenase complex confers a labile structure that is associated with its catalytic activity. PLoS One 2020;15:e0243489. [PMID: 33370314 PMCID: PMC7769281 DOI: 10.1371/journal.pone.0243489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/21/2020] [Indexed: 12/04/2022]  Open
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Rosenberger G, Heusel M, Bludau I, Collins BC, Martelli C, Williams EG, Xue P, Liu Y, Aebersold R, Califano A. SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. Cell Syst 2020;11:589-607.e8. [PMID: 33333029 PMCID: PMC8034988 DOI: 10.1016/j.cels.2020.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/25/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022]
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Ross AB, Langer JD, Jovanovic M. Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives. Mol Cell Proteomics 2020;20:100016. [PMID: 33556866 PMCID: PMC7950106 DOI: 10.1074/mcp.r120.002190] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/17/2023]  Open
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Peck Justice SA, Barron MP, Qi GD, Wijeratne HRS, Victorino JF, Simpson ER, Vilseck JZ, Wijeratne AB, Mosley AL. Mutant thermal proteome profiling for characterization of missense protein variants and their associated phenotypes within the proteome. J Biol Chem 2020;295:16219-16238. [PMID: 32878984 PMCID: PMC7705321 DOI: 10.1074/jbc.ra120.014576] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/17/2020] [Indexed: 12/20/2022]  Open
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Zablotskii V, Polyakova T, Dejneka A. Modulation of the Cell Membrane Potential and Intracellular Protein Transport by High Magnetic Fields. Bioelectromagnetics 2020;42:27-36. [PMID: 33179821 DOI: 10.1002/bem.22309] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/16/2020] [Accepted: 10/22/2020] [Indexed: 01/26/2023]
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Pang CNI, Ballouz S, Weissberger D, Thibaut LM, Hamey JJ, Gillis J, Wilkins MR, Hart-Smith G. Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes. Mol Cell Proteomics 2020;19:1876-1895. [PMID: 32817346 PMCID: PMC7664123 DOI: 10.1074/mcp.ra120.002154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/14/2020] [Indexed: 11/06/2022]  Open
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Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes. Nat Protoc 2020;15:2341-2386. [PMID: 32690956 DOI: 10.1038/s41596-020-0332-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 04/17/2020] [Indexed: 01/03/2023]
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McWhite CD, Papoulas O, Drew K, Cox RM, June V, Dong OX, Kwon T, Wan C, Salmi ML, Roux SJ, Browning KS, Chen ZJ, Ronald PC, Marcotte EM. A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. Cell 2020;181:460-474.e14. [PMID: 32191846 PMCID: PMC7297045 DOI: 10.1016/j.cell.2020.02.049] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/08/2020] [Accepted: 02/21/2020] [Indexed: 01/11/2023]
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Caudron-Herger M, Wassmer E, Nasa I, Schultz AS, Seiler J, Kettenbach AN, Diederichs S. Identification, quantification and bioinformatic analysis of RNA-dependent proteins by RNase treatment and density gradient ultracentrifugation using R-DeeP. Nat Protoc 2020;15:1338-1370. [PMID: 32094787 PMCID: PMC7212772 DOI: 10.1038/s41596-019-0261-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/29/2019] [Indexed: 12/14/2022]
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