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For: Jadot M, Boonen M, Thirion J, Wang N, Xing J, Zhao C, Tannous A, Qian M, Zheng H, Everett JK, Moore DF, Sleat DE, Lobel P. Accounting for Protein Subcellular Localization: A Compartmental Map of the Rat Liver Proteome. Mol Cell Proteomics 2016;16:194-212. [PMID: 27923875 DOI: 10.1074/mcp.m116.064527] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 11/18/2016] [Indexed: 11/06/2022]  Open
Number Cited by Other Article(s)
1
Hao H, Yuan Y, Ito A, Eberand BM, Tjondro H, Cielesh M, Norris N, Moreno CL, Maxwell JWC, Neely GG, Payne RJ, Kebede MA, Urbauer RJB, Passam FH, Larance M, Haltiwanger RS. FUT10 and FUT11 are protein O-fucosyltransferases that modify protein EMI domains. Nat Chem Biol 2025;21:598-610. [PMID: 39775168 PMCID: PMC11949838 DOI: 10.1038/s41589-024-01815-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: 02/06/2024] [Accepted: 12/04/2024] [Indexed: 01/11/2025]
2
Breckels LM, Hutchings C, Ingole KD, Kim S, Lilley KS, Makwana MV, McCaskie KJA, Villanueva E. Advances in spatial proteomics: Mapping proteome architecture from protein complexes to subcellular localizations. Cell Chem Biol 2024;31:1665-1687. [PMID: 39303701 DOI: 10.1016/j.chembiol.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]
3
Li Y, Zeng GH, Liang YJ, Yang HR, Zhu XL, Zhai YJ, Duan LX, Xu YY. Improving quantitative prediction of protein subcellular locations in fluorescence images through deep generative models. Comput Biol Med 2024;179:108913. [PMID: 39047508 DOI: 10.1016/j.compbiomed.2024.108913] [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: 04/15/2024] [Revised: 06/21/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
4
Bhushan V, Nita-Lazar A. Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology. J Proteome Res 2024;23:2700-2722. [PMID: 38451675 PMCID: PMC11296931 DOI: 10.1021/acs.jproteome.3c00839] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
5
Veszelyi K, Czegle I, Varga V, Németh CE, Besztercei B, Margittai É. Subcellular Localization of Thioredoxin/Thioredoxin Reductase System-A Missing Link in Endoplasmic Reticulum Redox Balance. Int J Mol Sci 2024;25:6647. [PMID: 38928353 PMCID: PMC11204020 DOI: 10.3390/ijms25126647] [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: 03/20/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]  Open
6
Huynh HT, Shcherbinina E, Huang HC, Rezaei R, Sarshad AA. Biochemical Separation of Cytoplasmic and Nuclear Fraction for Downstream Molecular Analysis. Curr Protoc 2024;4:e1042. [PMID: 38767195 DOI: 10.1002/cpz1.1042] [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: 05/22/2024]
7
Singin Ö, Astapenka A, Costina V, Kühl S, Bonekamp N, Drews O, Islinger M. Analysis of the Mouse Hepatic Peroxisome Proteome-Identification of Novel Protein Constituents Using a Semi-Quantitative SWATH-MS Approach. Cells 2024;13:176. [PMID: 38247867 PMCID: PMC10814758 DOI: 10.3390/cells13020176] [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: 12/21/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]  Open
8
Phukan H, Sarma A, Rex DAB, Christie SAD, Sabu SK, Hariharan S, Prasad TSK, Madanan MG. Physiological Temperature and Osmotic Changes Drive Dynamic Proteome Alterations in the Leptospiral Outer Membrane and Enhance Protein Export Systems. J Proteome Res 2023;22:3447-3463. [PMID: 37877620 DOI: 10.1021/acs.jproteome.3c00295] [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: 10/26/2023]
9
Moloney NM, Barylyuk K, Tromer E, Crook OM, Breckels LM, Lilley KS, Waller RF, MacGregor P. Mapping diversity in African trypanosomes using high resolution spatial proteomics. Nat Commun 2023;14:4401. [PMID: 37479728 PMCID: PMC10361982 DOI: 10.1038/s41467-023-40125-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 07/06/2023] [Indexed: 07/23/2023]  Open
10
Akter F, Bonini S, Ponnaiyan S, Kögler-Mohrbacher B, Bleibaum F, Damme M, Renard BY, Winter D. Multi-Cell Line Analysis of Lysosomal Proteomes Reveals Unique Features and Novel Lysosomal Proteins. Mol Cell Proteomics 2023;22:100509. [PMID: 36791992 PMCID: PMC10025164 DOI: 10.1016/j.mcpro.2023.100509] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023]  Open
11
Alles J, Legnini I, Pacelli M, Rajewsky N. Rapid nuclear deadenylation of mammalian messenger RNA. iScience 2022;26:105878. [PMID: 36691625 PMCID: PMC9860345 DOI: 10.1016/j.isci.2022.105878] [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: 01/26/2022] [Revised: 06/13/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]  Open
12
Mou M, Pan Z, Lu M, Sun H, Wang Y, Luo Y, Zhu F. Application of Machine Learning in Spatial Proteomics. J Chem Inf Model 2022;62:5875-5895. [PMID: 36378082 DOI: 10.1021/acs.jcim.2c01161] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
13
Crook OM, Lilley KS, Gatto L, Kirk PD. Semi-Supervised Non-Parametric Bayesian Modelling of Spatial Proteomics. Ann Appl Stat 2022;16:22-aoas1603. [PMID: 36507469 PMCID: PMC7613899 DOI: 10.1214/22-aoas1603] [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] [Indexed: 02/02/2023]
14
Rusilowicz-Jones EV, Brazel AJ, Frigenti F, Urbé S, Clague MJ. Membrane compartmentalisation of the ubiquitin system. Semin Cell Dev Biol 2022;132:171-184. [PMID: 34895815 DOI: 10.1016/j.semcdb.2021.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 12/15/2022]
15
Batzios S, Tal G, DiStasio AT, Peng Y, Charalambous C, Nicolaides P, Kamsteeg EJ, Korman SH, Mandel H, Steinbach PJ, Yi L, Fair SR, Hester ME, Drousiotou A, Kaler SG. Newly identified disorder of copper metabolism caused by variants in CTR1, a high-affinity copper transporter. Hum Mol Genet 2022;31:4121-4130. [PMID: 35913762 PMCID: PMC9759326 DOI: 10.1093/hmg/ddac156] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 01/21/2023]  Open
16
Lao Y, Li Y, Wang W, Ren L, Qian X, He F, Chen X, Jiang Y. A Cytological Atlas of the Human Liver Proteome from PROTEOMESKY-LIVERHu 2.0, a Publicly Available Database. J Proteome Res 2022;21:1916-1929. [PMID: 35820117 DOI: 10.1021/acs.jproteome.2c00190] [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]
17
Moore DF, Sleat DE, Lobel P. A Method to Estimate the Distribution of Proteins across Multiple Compartments Using Data from Quantitative Proteomics Subcellular Fractionation Experiments. J Proteome Res 2022;21:1371-1381. [PMID: 35522998 DOI: 10.1021/acs.jproteome.1c00781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
18
Meng D, Yang Q, Jeong MH, Curukovic A, Tiwary S, Melick CH, Lama-Sherpa TD, Wang H, Huerta-Rosario M, Urquhart G, Zacharias LG, Lewis C, DeBerardinis RJ, Jewell JL. SNAT7 regulates mTORC1 via macropinocytosis. Proc Natl Acad Sci U S A 2022;119:e2123261119. [PMID: 35561222 PMCID: PMC9171778 DOI: 10.1073/pnas.2123261119] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/13/2022] [Indexed: 11/30/2022]  Open
19
Torres-Sangiao E, Giddey AD, Leal Rodriguez C, Tang Z, Liu X, Soares NC. Proteomic Approaches to Unravel Mechanisms of Antibiotic Resistance and Immune Evasion of Bacterial Pathogens. Front Med (Lausanne) 2022;9:850374. [PMID: 35586072 PMCID: PMC9108449 DOI: 10.3389/fmed.2022.850374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022]  Open
20
Barral DC, Staiano L, Guimas Almeida C, Cutler DF, Eden ER, Futter CE, Galione A, Marques ARA, Medina DL, Napolitano G, Settembre C, Vieira OV, Aerts JMFG, Atakpa‐Adaji P, Bruno G, Capuozzo A, De Leonibus E, Di Malta C, Escrevente C, Esposito A, Grumati P, Hall MJ, Teodoro RO, Lopes SS, Luzio JP, Monfregola J, Montefusco S, Platt FM, Polishchuck R, De Risi M, Sambri I, Soldati C, Seabra MC. Current methods to analyze lysosome morphology, positioning, motility and function. Traffic 2022;23:238-269. [PMID: 35343629 PMCID: PMC9323414 DOI: 10.1111/tra.12839] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 01/09/2023]
21
p38-MAPK recruits the proteolytic pathways in Caenorhabditis elegans during bacterial infection. Int J Biol Macromol 2022;204:116-135. [PMID: 35124023 DOI: 10.1016/j.ijbiomac.2022.01.191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 11/21/2022]
22
Elzek MAW, Christopher JA, Breckels LM, Lilley KS. Localization of Organelle Proteins by Isotope Tagging: Current status and potential applications in drug discovery research. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021;39:57-67. [PMID: 34906326 DOI: 10.1016/j.ddtec.2021.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/26/2021] [Accepted: 06/11/2021] [Indexed: 12/18/2022]
23
Mulvey CM, Breckels LM, Crook OM, Sanders DJ, Ribeiro ALR, Geladaki A, Christoforou A, Britovšek NK, Hurrell T, Deery MJ, Gatto L, Smith AM, Lilley KS. Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line. Nat Commun 2021;12:5773. [PMID: 34599159 PMCID: PMC8486773 DOI: 10.1038/s41467-021-26000-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 09/07/2021] [Indexed: 02/07/2023]  Open
24
Lyu Z, Genereux JC. Methodologies for Measuring Protein Trafficking across Cellular Membranes. Chempluschem 2021;86:1397-1415. [PMID: 34636167 DOI: 10.1002/cplu.202100304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/19/2021] [Indexed: 12/11/2022]
25
Seif Y, Palsson BØ. Path to improving the life cycle and quality of genome-scale models of metabolism. Cell Syst 2021;12:842-859. [PMID: 34555324 PMCID: PMC8480436 DOI: 10.1016/j.cels.2021.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 02/17/2021] [Accepted: 06/23/2021] [Indexed: 11/28/2022]
26
Dewulf JP, Paquay S, Marbaix E, Achouri Y, Van Schaftingen E, Bommer GT. ECHDC1 knockout mice accumulate ethyl-branched lipids and excrete abnormal intermediates of branched-chain fatty acid metabolism. J Biol Chem 2021;297:101083. [PMID: 34419447 PMCID: PMC8473548 DOI: 10.1016/j.jbc.2021.101083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/15/2022]  Open
27
Christopher JA, Stadler C, Martin CE, Morgenstern M, Pan Y, Betsinger CN, Rattray DG, Mahdessian D, Gingras AC, Warscheid B, Lehtiö J, Cristea IM, Foster LJ, Emili A, Lilley KS. Subcellular proteomics. NATURE REVIEWS. METHODS PRIMERS 2021;1:32. [PMID: 34549195 PMCID: PMC8451152 DOI: 10.1038/s43586-021-00029-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/15/2021] [Indexed: 12/11/2022]
28
Clague MJ, Urbé S. Data mining for traffic information. Traffic 2021;21:162-168. [PMID: 31596015 DOI: 10.1111/tra.12702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 12/23/2022]
29
Gao ZF, Shen Z, Chao Q, Yan Z, Ge XL, Lu T, Zheng H, Qian CR, Wang BC. Large-scale Proteomic and Phosphoproteomic Analyses of Maize Seedling Leaves During De-etiolation. GENOMICS PROTEOMICS & BIOINFORMATICS 2020;18:397-414. [PMID: 33385613 PMCID: PMC8242269 DOI: 10.1016/j.gpb.2020.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/16/2019] [Accepted: 05/12/2020] [Indexed: 12/20/2022]
30
Imai K, Nakai K. Tools for the Recognition of Sorting Signals and the Prediction of Subcellular Localization of Proteins From Their Amino Acid Sequences. Front Genet 2020;11:607812. [PMID: 33324450 PMCID: PMC7723863 DOI: 10.3389/fgene.2020.607812] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022]  Open
31
Pérez-Rodriguez S, de Jesús Ramírez-Lira M, Wulff T, Voldbor BG, Ramírez OT, Trujillo-Roldán MA, Valdez-Cruz NA. Enrichment of microsomes from Chinese hamster ovary cells by subcellular fractionation for its use in proteomic analysis. PLoS One 2020;15:e0237930. [PMID: 32841274 PMCID: PMC7447005 DOI: 10.1371/journal.pone.0237930] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/06/2020] [Indexed: 11/19/2022]  Open
32
Borner GHH. Organellar Maps Through Proteomic Profiling - A Conceptual Guide. Mol Cell Proteomics 2020;19:1076-1087. [PMID: 32345598 PMCID: PMC7338086 DOI: 10.1074/mcp.r120.001971] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/27/2020] [Indexed: 11/29/2022]  Open
33
Crook OM, Smith T, Elzek M, Lilley KS. Moving Profiling Spatial Proteomics Beyond Discrete Classification. Proteomics 2020;20:e1900392. [PMID: 32558233 DOI: 10.1002/pmic.201900392] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/18/2020] [Indexed: 12/12/2022]
34
Tannous A, Boonen M, Zheng H, Zhao C, Germain CJ, Moore DF, Sleat DE, Jadot M, Lobel P. Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics. J Proteome Res 2020;19:1718-1730. [PMID: 32134668 DOI: 10.1021/acs.jproteome.9b00862] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
35
Lundberg E, Borner GHH. Spatial proteomics: a powerful discovery tool for cell biology. Nat Rev Mol Cell Biol 2020;20:285-302. [PMID: 30659282 DOI: 10.1038/s41580-018-0094-y] [Citation(s) in RCA: 342] [Impact Index Per Article: 68.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
36
Wegler C, Ölander M, Wiśniewski JR, Lundquist P, Zettl K, Åsberg A, Hjelmesæth J, Andersson TB, Artursson P. Global variability analysis of mRNA and protein concentrations across and within human tissues. NAR Genom Bioinform 2020;2:lqz010. [PMID: 33575562 PMCID: PMC7671341 DOI: 10.1093/nargab/lqz010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/27/2019] [Accepted: 10/06/2019] [Indexed: 12/25/2022]  Open
37
Collier AM, Nemtsova Y, Kuber N, Banach-Petrosky W, Modak A, Sleat DE, Nanda V, Lobel P. Lysosomal protein thermal stability does not correlate with cellular half-life: global observations and a case study of tripeptidyl-peptidase 1. Biochem J 2020;477:727-745. [PMID: 31957806 PMCID: PMC8442665 DOI: 10.1042/bcj20190874] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/16/2022]
38
Joshi RN, Stadler C, Lehmann R, Lehtiö J, Tegnér J, Schmidt A, Vesterlund M. TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells. Front Immunol 2019;10:2708. [PMID: 31849937 PMCID: PMC6902019 DOI: 10.3389/fimmu.2019.02708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/04/2019] [Indexed: 01/07/2023]  Open
39
Sleat DE, Wiseman JA, El-Banna M, Zheng H, Zhao C, Soherwardy A, Moore DF, Lobel P. Analysis of Brain and Cerebrospinal Fluid from Mouse Models of the Three Major Forms of Neuronal Ceroid Lipofuscinosis Reveals Changes in the Lysosomal Proteome. Mol Cell Proteomics 2019;18:2244-2261. [PMID: 31501224 PMCID: PMC6823856 DOI: 10.1074/mcp.ra119.001587] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/06/2019] [Indexed: 01/06/2023]  Open
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The synthesis of branched-chain fatty acids is limited by enzymatic decarboxylation of ethyl- and methylmalonyl-CoA. Biochem J 2019;476:2427-2447. [PMID: 31416829 PMCID: PMC6717113 DOI: 10.1042/bcj20190500] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/12/2019] [Accepted: 08/15/2019] [Indexed: 11/17/2022]
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Nightingale DJH, Lilley KS, Oliver SG. A Protocol to Map the Spatial Proteome Using HyperLOPIT in Saccharomyces cerevisiae. Bio Protoc 2019;9:e3303. [PMID: 33654815 PMCID: PMC7854154 DOI: 10.21769/bioprotoc.3303] [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: 03/26/2019] [Revised: 05/12/2019] [Accepted: 06/25/2019] [Indexed: 11/02/2022]  Open
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Costello JL, Passmore JB, Islinger M, Schrader M. Multi-localized Proteins: The Peroxisome-Mitochondria Connection. Subcell Biochem 2019;89:383-415. [PMID: 30378033 DOI: 10.1007/978-981-13-2233-4_17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Crook OM, Breckels LM, Lilley KS, Kirk PD, Gatto L. A Bioconductor workflow for the Bayesian analysis of spatial proteomics. F1000Res 2019;8:446. [PMID: 31119032 PMCID: PMC6509962 DOI: 10.12688/f1000research.18636.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/25/2019] [Indexed: 02/02/2023]  Open
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Yang W, Zhu XJ, Huang J, Ding H, Lin H. A Brief Survey of Machine Learning Methods in Protein Sub-Golgi Localization. Curr Bioinform 2019. [DOI: 10.2174/1574893613666181113131415] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Geladaki A, Kočevar Britovšek N, Breckels LM, Smith TS, Vennard OL, Mulvey CM, Crook OM, Gatto L, Lilley KS. Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. Nat Commun 2019;10:331. [PMID: 30659192 PMCID: PMC6338729 DOI: 10.1038/s41467-018-08191-w] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/18/2018] [Indexed: 01/09/2023]  Open
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Nguyen T, Pappireddi N, Wühr M. Proteomics of nucleocytoplasmic partitioning. Curr Opin Chem Biol 2018;48:55-63. [PMID: 30472625 DOI: 10.1016/j.cbpa.2018.10.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/21/2022]
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Marginal protein stability drives subcellular proteome isoelectric point. Proc Natl Acad Sci U S A 2018;115:11778-11783. [PMID: 30385634 DOI: 10.1073/pnas.1809098115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
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Pires HR, Boxem M. Mapping the Polarity Interactome. J Mol Biol 2018;430:3521-3544. [DOI: 10.1016/j.jmb.2017.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/14/2017] [Accepted: 12/18/2017] [Indexed: 12/11/2022]
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Amick J, Tharkeshwar AK, Amaya C, Ferguson SM. WDR41 supports lysosomal response to changes in amino acid availability. Mol Biol Cell 2018;29:2213-2227. [PMID: 29995611 PMCID: PMC6249801 DOI: 10.1091/mbc.e17-12-0703] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
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Miklosi AG, Del Favero G, Marko D, Harkany T, Lubec G. Resolution Matters: Correlating Quantitative Proteomics and Nanoscale-Precision Microscopy for Reconstructing Synapse Identity. Proteomics 2018;18:e1800139. [PMID: 29932496 PMCID: PMC6099515 DOI: 10.1002/pmic.201800139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/11/2018] [Indexed: 11/25/2022]
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