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McGann CD, Barshop WD, Canterbury JD, Lin C, Gabriel W, Huang J, Bergen D, Zabrouskov V, Melani RD, Wilhelm M, McAlister GC, Schweppe DK. Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics. J Proteome Res 2023; 22:2836-2846. [PMID: 37557900 DOI: 10.1021/acs.jproteome.3c00085] [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: 08/11/2023]
Abstract
Sample multiplexed quantitative proteomics assays have proved to be a highly versatile means to assay molecular phenotypes. Yet, stochastic precursor selection and precursor coisolation can dramatically reduce the efficiency of data acquisition and quantitative accuracy. To address this, intelligent data acquisition (IDA) strategies have recently been developed to improve instrument efficiency and quantitative accuracy for both discovery and targeted methods. Toward this end, we sought to develop and implement a new real-time spectral library searching (RTLS) workflow that could enable intelligent scan triggering and peak selection within milliseconds of scan acquisition. To ensure ease of use and general applicability, we built an application to read in diverse spectral libraries and file types from both empirical and predicted spectral libraries. We demonstrate that RTLS methods enable improved quantitation of multiplexed samples, particularly with consideration for quantitation from chimeric fragment spectra. We used RTLS to profile proteome responses to small molecule perturbations and were able to quantify up to 15% more significantly regulated proteins in half the gradient time compared to traditional methods. Taken together, the development of RTLS expands the IDA toolbox to improve instrument efficiency and quantitative accuracy for sample multiplexed analyses.
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Affiliation(s)
- Chris D McGann
- University of Washington, Seattle, Washington 98105, United States
| | | | | | - Chuwei Lin
- University of Washington, Seattle, Washington 98105, United States
| | | | - Jingjing Huang
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - David Bergen
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Rafael D Melani
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | | | - Devin K Schweppe
- University of Washington, Seattle, Washington 98105, United States
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Ma Z, Li W, Zhuang L, Wen T, Wang P, Yu H, Liu Y, Yu Y. TMEM59 ablation leads to loss of olfactory sensory neurons and impairs olfactory functions via interaction with inflammation. Brain Behav Immun 2023; 111:151-168. [PMID: 37061103 DOI: 10.1016/j.bbi.2023.04.005] [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: 12/22/2022] [Revised: 03/23/2023] [Accepted: 04/11/2023] [Indexed: 04/17/2023] Open
Abstract
The olfactory epithelium undergoes constant neurogenesis throughout life in mammals. Several factors including key signaling pathways and inflammatory microenvironment regulate the maintenance and regeneration of the olfactory epithelium. In this study, we identify TMEM59 (also known as DCF1) as a critical regulator to the epithelial maintenance and regeneration. Single-cell RNA-Seq data show downregulation of TMEM59 in multiple epithelial cell lineages with aging. Ablation of TMEM59 leads to apparent alteration at the transcriptional level, including genes associated with olfactory transduction and inflammatory/immune response. These differentially expressed genes are key components belonging to several signaling pathways, such as NF-κB, chemokine, etc. TMEM59 deletion impairs olfactory functions, attenuates proliferation, causes loss of both mature and immature olfactory sensory neurons, and promotes infiltration of inflammatory cells, macrophages, microglia cells and neutrophils into the olfactory epithelium and lamina propria. TMEM59 deletion deteriorates regeneration of the olfactory epithelium after injury, with significant reduction in the number of proliferative cells, immature and mature sensory neurons, accompanied by the increasing number of inflammatory cells and macrophages. Anti-inflammation by dexamethasone recovers neuronal generation and olfactory functions in the TMEM59-KO animals, suggesting the correlation between TMEM59 and inflammation in regulating the epithelial maintenance. Collectively, TMEM59 regulates olfactory functions, as well as neuronal generation in the olfactory epithelium via interaction with inflammation, suggesting a potential role in therapy against olfactory dysfunction associated with inflamm-aging.
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Affiliation(s)
- Zhenjie Ma
- School of Life Sciences, Shanghai University, Shanghai, People's Republic of China
| | - Weihao Li
- Department of Otolaryngology, Eye, Ear, Nose & Throat Hospital, Fudan University, Shanghai, People's Republic of China; Ear, Nose & Throat Institute, Eye, Ear, Nose & Throat Hospital, Fudan University, Shanghai, People's Republic of China; Clinical and Research Center for Olfactory Disorders, Eye, Ear, Nose & Throat Hospital, Fudan University, Shanghai, People's Republic of China
| | - Liujing Zhuang
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China; The MOE Frontier Science Center for Brain Science & Brain-machine Integration, Zhejiang University, Hangzhou 310027, China
| | - Tieqiao Wen
- School of Life Sciences, Shanghai University, Shanghai, People's Republic of China
| | - Ping Wang
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China; The MOE Frontier Science Center for Brain Science & Brain-machine Integration, Zhejiang University, Hangzhou 310027, China.
| | - Hongmeng Yu
- Department of Otolaryngology, Eye, Ear, Nose & Throat Hospital, Fudan University, Shanghai, People's Republic of China; Ear, Nose & Throat Institute, Eye, Ear, Nose & Throat Hospital, Fudan University, Shanghai, People's Republic of China; Clinical and Research Center for Olfactory Disorders, Eye, Ear, Nose & Throat Hospital, Fudan University, Shanghai, People's Republic of China.
| | - Yongliang Liu
- Department of Otolaryngology, Zibo Central Hospital, Zibo 255036, China.
| | - Yiqun Yu
- Department of Otolaryngology, Eye, Ear, Nose & Throat Hospital, Fudan University, Shanghai, People's Republic of China; Ear, Nose & Throat Institute, Eye, Ear, Nose & Throat Hospital, Fudan University, Shanghai, People's Republic of China; Clinical and Research Center for Olfactory Disorders, Eye, Ear, Nose & Throat Hospital, Fudan University, Shanghai, People's Republic of China.
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