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For: Srivastava S, Merchant M, Rai A, Rai SN. Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry: Technical and Statistical Considerations. J Proteomics Bioinform 2019;12:48-55. [PMID: 32148359 PMCID: PMC7059694 DOI: 10.35248/0974-276x.19.12.496] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Number Cited by Other Article(s)
1
Kremer JL, Sanchez Ortega H, Souza-Siqueira T, Blanes Angeli C, Kei Iwai L, Palmisano G, Ferini Pacicco Lotfi C. Proteomic profiling of the extracellular matrix in the human adrenal cortex. Matrix Biol Plus 2024;23:100158. [PMID: 39188294 PMCID: PMC11345916 DOI: 10.1016/j.mbplus.2024.100158] [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: 04/20/2024] [Revised: 07/09/2024] [Accepted: 07/25/2024] [Indexed: 08/28/2024]  Open
2
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
3
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 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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
4
Brady A, Sheneman KR, Pulsifer AR, Price SL, Garrison TM, Maddipati KR, Bodduluri SR, Pan J, Boyd NL, Zheng JJ, Rai SN, Hellmann J, Haribabu B, Uriarte SM, Lawrenz MB. Type 3 secretion system induced leukotriene B4 synthesis by leukocytes is actively inhibited by Yersinia pestis to evade early immune recognition. PLoS Pathog 2024;20:e1011280. [PMID: 38271464 PMCID: PMC10846697 DOI: 10.1371/journal.ppat.1011280] [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: 03/12/2023] [Revised: 02/06/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024]  Open
5
Elnagdy M, Wang Y, Rodriguez W, Zhang J, Bauer P, Wilkey DW, Merchant M, Pan J, Farooqui Z, Cannon R, Rai S, Maldonado C, Barve S, McClain CJ, Gobejishvili L. Increased expression of phosphodiesterase 4 in activated hepatic stellate cells promotes cytoskeleton remodeling and cell migration. J Pathol 2023;261:361-371. [PMID: 37735782 PMCID: PMC10653049 DOI: 10.1002/path.6194] [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: 02/12/2023] [Revised: 06/24/2023] [Accepted: 07/30/2023] [Indexed: 09/23/2023]
6
Piell KM, Petri BJ, Head KZ, Wahlang B, Xu R, Zhang X, Pan J, Rai SN, de Silva K, Chariker JH, Rouchka EC, Tan M, Li Y, Cave MC, Klinge CM. Disruption of the mouse liver epitranscriptome by long-term aroclor 1260 exposure. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023;100:104138. [PMID: 37137421 PMCID: PMC10330322 DOI: 10.1016/j.etap.2023.104138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/26/2023] [Accepted: 04/29/2023] [Indexed: 05/05/2023]
7
An Optimized Comparative Proteomic Approach as a Tool in Neurodegenerative Disease Research. Cells 2022;11:cells11172653. [PMID: 36078061 PMCID: PMC9454658 DOI: 10.3390/cells11172653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022]  Open
8
Petri BJ, Piell KM, Wahlang B, Head KZ, Andreeva K, Rouchka EC, Pan J, Rai SN, Cave MC, Klinge CM. Multiomics analysis of the impact of polychlorinated biphenyls on environmental liver disease in a mouse model. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2022;94:103928. [PMID: 35803474 DOI: 10.1016/j.etap.2022.103928] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/27/2022] [Accepted: 07/03/2022] [Indexed: 06/15/2023]
9
Jin J, Wahlang B, Thapa M, Head KZ, Hardesty JE, Srivastava S, Merchant ML, Rai SN, Prough RA, Cave MC. Proteomics and metabolic phenotyping define principal roles for the aryl hydrocarbon receptor in mouse liver. Acta Pharm Sin B 2021;11:3806-3819. [PMID: 35024308 PMCID: PMC8727924 DOI: 10.1016/j.apsb.2021.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/20/2022]  Open
10
Klinge CM, Piell KM, Petri BJ, He L, Zhang X, Pan J, Rai SN, Andreeva K, Rouchka EC, Wahlang B, Beier JI, Cave MC. Combined exposure to polychlorinated biphenyls and high-fat diet modifies the global epitranscriptomic landscape in mouse liver. ENVIRONMENTAL EPIGENETICS 2021;7:dvab008. [PMID: 34548932 PMCID: PMC8448424 DOI: 10.1093/eep/dvab008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/13/2021] [Accepted: 08/10/2021] [Indexed: 05/30/2023]
11
García-Vence M, Chantada-Vazquez MDP, Sosa-Fajardo A, Agra R, Barcia de la Iglesia A, Otero-Glez A, García-González M, Cameselle-Teijeiro JM, Nuñez C, Bravo JJ, Bravo SB. Protein Extraction From FFPE Kidney Tissue Samples: A Review of the Literature and Characterization of Techniques. Front Med (Lausanne) 2021;8:657313. [PMID: 34055835 PMCID: PMC8158658 DOI: 10.3389/fmed.2021.657313] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022]  Open
12
Morgenstern D, Barzilay R, Levin Y. RawBeans: A Simple, Vendor-Independent, Raw-Data Quality-Control Tool. J Proteome Res 2021;20:2098-2104. [PMID: 33657803 PMCID: PMC8041395 DOI: 10.1021/acs.jproteome.0c00956] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
13
Jin J, Wahlang B, Shi H, Hardesty JE, Falkner KC, Head KZ, Srivastava S, Merchant ML, Rai SN, Cave MC, Prough RA. Dioxin-like and non-dioxin-like PCBs differentially regulate the hepatic proteome and modify diet-induced nonalcoholic fatty liver disease severity. Med Chem Res 2020;29:1247-1263. [PMID: 32831531 PMCID: PMC7440142 DOI: 10.1007/s00044-020-02581-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/30/2020] [Indexed: 02/06/2023]
14
Merchant ML, Barati MT, Caster DJ, Hata JL, Hobeika L, Coventry S, Brier ME, Wilkey DW, Li M, Rood IM, Deegens JK, Wetzels JF, Larsen CP, Troost JP, Hodgin JB, Mariani LH, Kretzler M, Klein JB, McLeish KR. Proteomic Analysis Identifies Distinct Glomerular Extracellular Matrix in Collapsing Focal Segmental Glomerulosclerosis. J Am Soc Nephrol 2020;31:1883-1904. [PMID: 32561683 DOI: 10.1681/asn.2019070696] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 04/13/2020] [Indexed: 12/28/2022]  Open
15
Microbiome data analysis with applications to pre-clinical studies using QIIME2: Statistical considerations. Genes Dis 2019;8:215-223. [PMID: 33997168 PMCID: PMC8099687 DOI: 10.1016/j.gendis.2019.12.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/14/2019] [Indexed: 11/28/2022]  Open
16
Interactive Web Tool for Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry Data. JOURNAL OF PROTEOMICS & BIOINFORMATICS 2019;12:85-88. [PMID: 32148360 PMCID: PMC7059686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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