A new photolabeling probe for efficient enrichment and deep profiling of cell surface membrane proteome by mass spectrometry

Li, Yuanyuan; Xia, Chaoshuang; Zhao, Hongxian; Xie, Yunying; Zhang, Yangjun; Zhang, Wanjun; Yu, Yong-Liang; Wang, Jianhua; Qin, Weijie

doi:10.1016/j.cclet.2022.03.100

Cited by 8 publications

(6 citation statements)

References 34 publications

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“…The suppression of genes for root development and pathogen response is a common consequence of abiotic stress [43]. There are reviews of further works that support these findings [44,45]. In a similar vein, additional research has shown that in Arabidopsis thaliana seedlings, gene expression for the peroxide-scavenging enzyme was influenced by CNTs [46].…”

Section: Introductionmentioning

confidence: 93%

Plant–Nanoparticle Interactions: Transcriptomic and Proteomic Insights

Munir,

Gulzar,

Abideen

et al. 2023

Agronomy

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In recent years, the relationship between plants and nanoparticles (NPs) has been the subject of extensive research interest. Hence, an ever-increasing number of perspectives connected with both the positive and adverse consequences of NPs application in plants are highlighted in this review. On the other hand, nanoparticles and their interactive effects on plants have raised concern regarding their harmful aspects. There are complex mechanisms evolved in plants for controlling the uptake, accumulation, and mobilization of nanoparticles that need to be discussed further, especially in the context of proteomics and genetic level. To fill this gap, there is a dire need for the integration and application of multiomics in plants to identify sensitive biomarkers responding to engineered NPs and to provide mechanistic insights in order to design safer and enhanced nano-enabled products for agriculture. For this purpose, transcriptomic technologies have essentially contributed to understanding of the molecular systems in plants against nanoparticle stress by laying out an association between gene expression and cell response. In light of this background, the current article attempts to summarize a variety of recent transcriptomic and proteomic contributions that have been made to establishing the genetic basis of nanoparticle uptake and the mechanism of stress response. The present article also looks at recent proteomic and transcriptomic studies to learn more about the intricate regulatory network that connects plant and nanoparticle stress responses.

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Section: Introductionmentioning

confidence: 93%

Plant–Nanoparticle Interactions: Transcriptomic and Proteomic Insights

Munir,

Gulzar,

Abideen

et al. 2023

Agronomy

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“…N -Glycosylation is a universal and essential PTM of proteins that mediates a wide variety of key biological processes involved in intercellular recognition, signal transduction, immune response, − and the occurrence and development of diseases . Altered N -glycosylation profiles have been found in many malignant cancers and other diseases, making comprehensive characterization of protein N -glycosylation critical to improve our understanding of health and disease. − Intact N -glycopeptide characterization that provides both the N -glycan structure and the glycosylation site is a useful tool for composition and function elucidation of the N -glycoproteome. − Currently, liquid chromatography–tandem mass spectrometry (LC–MS/MS) is the method of choice for intact N -glycopeptide characterization. − ,− Due to the low abundance of N -glycopeptides in complex biological samples and the ion suppression effects of coeluting non-glycopeptides in LC–MS analysis, N -glycopeptide enrichment is necessary for large-scale intact N -glycopeptide analysis. ,,− Efficient enrichment and comprehensive intact N -glycopeptide profiling requires a large amount of starting material (dozens to hundreds of micrograms of peptide samples), which is incompatible with studies on single or rare cells, such as tumor stem cells and circulating tumor cells. Currently, the lack of sufficiently sensitive methods is the major bottleneck limiting the study of cell heterogeneity of N -glycosylation and hindering its application in immune cell subtype research and tumor immunotherapy.…”

Section: Introductionmentioning

confidence: 99%

Sensitive N-Glycopeptide Profiling of Single and Rare Cells Using an Isobaric Labeling Strategy without Enrichment

Kong

Fang

et al. 2023

Anal. Chem.

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Single-cell omics is critical in revealing population heterogeneity, discovering unique features of individual cells, and identifying minority subpopulations of interest. As one of the major post-translational modifications, protein N-glycosylation plays crucial roles in various important biological processes. Elucidation of the variation in N-glycosylation patterns at single-cell resolution may largely facilitate the understanding of their key roles in the tumor microenvironment and immune therapy. However, comprehensive N-glycoproteome profiling for single cells has not been achieved due to the extremely limited sample amount and incompatibility with the available enrichment strategies. Here, we have developed an isobaric labeling-based carrier strategy for highly sensitive intact N-glycopeptide profiling for single cells or a small number of rare cells without enrichment. Isobaric labeling has unique multiplexing properties, by which the “total” signal from all channels triggers MS/MS fragmentation for N-glycopeptide identification, while the reporter ions provide quantitative information. In our strategy, a carrier channel using N-glycopeptides obtained from bulk-cell samples significantly improved the “total” signal of N-glycopeptides and, therefore, promoted the first quantitative analysis of averagely 260 N-glycopeptides from single HeLa cells. We further applied this strategy to study the regional heterogeneity of N-glycosylation of microglia in mouse brain and discovered region-specific N-glycoproteome patterns and cell subtypes. In conclusion, the glycocarrier strategy provides an attractive solution for sensitive and quantitative N-glycopeptide profiling of single/rare cells that cannot be enriched by traditional workflows.

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“…The rapidly developing mass spectrometry (MS) techniques have revolutionized omics studies, including metabolomics 1,2 lipidomics 3,4 and proteomics. 5–8 Because proteins are the building blocks of life, proteomics is essential for understanding biological processes and dynamic networks. MS-based proteomic approaches have enabled the simultaneous investigation of thousands of proteins from complex biological samples.…”

Section: Introductionmentioning

confidence: 99%