TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing

Li, Jiaming; Cai, Zhenying; Bomgarden, Ryan; Pike, Ian; Kuhn, Karsten; Rogers, John C.; Roberts, Thomas M.; Gygi, Steven P.; Paulo, João A.

doi:10.1021/acs.jproteome.1c00168

Cited by 197 publications

(179 citation statements)

References 39 publications

(85 reference statements)

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“…To overcome this limitation, isobaric peptide labeling methods, such as iTRAQ [ 121 ], TMT [ 122 ] and DiLeu [ 123 ], have been developed to generate isobaric MS1 peaks and enable multiplexed tagging (e.g. 11-plex, 16-plex, 18-plex, and 27-plex TMT) [ 76 , 124 , 125 ]. After fragmentation of the isobaric peaks, different reporter ions are released for relative quantification in MS2/3 scans [ 126 ].…”

Section: The Evolving Technologies Of Protein Analysis and Mass Spectrometrymentioning

confidence: 99%

Proteomic landscape of Alzheimer’s Disease: novel insights into pathogenesis and biomarker discovery

Bai

Vanderwall

et al. 2021

Mol Neurodegeneration

132

100

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Mass spectrometry-based proteomics empowers deep profiling of proteome and protein posttranslational modifications (PTMs) in Alzheimer’s disease (AD). Here we review the advances and limitations in historic and recent AD proteomic research. Complementary to genetic mapping, proteomic studies not only validate canonical amyloid and tau pathways, but also uncover novel components in broad protein networks, such as RNA splicing, development, immunity, membrane transport, lipid metabolism, synaptic function, and mitochondrial activity. Meta-analysis of seven deep datasets reveals 2,698 differentially expressed (DE) proteins in the landscape of AD brain proteome (n = 12,017 proteins/genes), covering 35 reported AD genes and risk loci. The DE proteins contain cellular markers enriched in neurons, microglia, astrocytes, oligodendrocytes, and epithelial cells, supporting the involvement of diverse cell types in AD pathology. We discuss the hypothesized protective or detrimental roles of selected DE proteins, emphasizing top proteins in “amyloidome” (all biomolecules in amyloid plaques) and disease progression. Comprehensive PTM analysis represents another layer of molecular events in AD. In particular, tau PTMs are correlated with disease stages and indicate the heterogeneity of individual AD patients. Moreover, the unprecedented proteomic coverage of biofluids, such as cerebrospinal fluid and serum, procures novel putative AD biomarkers through meta-analysis. Thus, proteomics-driven systems biology presents a new frontier to link genotype, proteotype, and phenotype, accelerating the development of improved AD models and treatment strategies.

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Section: The Evolving Technologies Of Protein Analysis and Mass Spectrometrymentioning

confidence: 99%

Proteomic landscape of Alzheimer’s Disease: novel insights into pathogenesis and biomarker discovery

Bai

Vanderwall

et al. 2021

Mol Neurodegeneration

132

100

View full text Add to dashboard Cite

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“…purification, fractionation, solving, loading, and LC-separation affect the mixed samples equally. The current available isobaric chemical tags facilitate the simultaneous analysis of up to 18 experimental samples 83 , which significantly enhances throughput and reduces turnaround time. Moreover, isobaric labeling can be easily adapted for high-throughput measurements as sample preparation can be parallelized and automated.…”

Section: Discussionmentioning

confidence: 99%

Tryptophan metabolism is inversely regulated in the tumor and blood of patients with glioblastoma

Panitz¹,

Koncarevic²,

Sadik³

et al. 2021

Theranostics

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Tryptophan (Trp)-catabolic enzymes (TCEs) produce metabolites that activate the aryl hydrocarbon receptor (AHR) and promote tumor progression and immunosuppression in glioblastoma. As therapies targeting TCEs or AHR become available, a better understanding of Trp metabolism is required. Methods: The combination of LC-MS/MS with chemical isobaric labeling enabled the simultaneous quantitative comparison of Trp and its amino group-bearing metabolites in multiple samples. We applied this method to the sera of a cohort of 43 recurrent glioblastoma patients and 43 age- and sex-matched healthy controls. Tumor volumes were measured in MRI data using an artificial neural network-based approach. MALDI MSI visualized Trp and its direct metabolite N -formylkynurenine (FK) in glioblastoma tissue. Analysis of scRNA-seq data was used to detect the presence of Trp metabolism and AHR activity in different cell types in glioblastoma. Results: Compared to healthy controls, glioblastoma patients showed decreased serum Trp levels. Surprisingly, the levels of Trp metabolites were also reduced. The decrease became smaller with more enzymatic steps between Trp and its metabolites, suggesting that Trp availability controls the levels of its systemic metabolites. High tumor volume associated with low systemic metabolite levels and low systemic kynurenine levels associated with worse overall survival. MALDI MSI demonstrated heterogeneity of Trp catabolism across glioblastoma tissues. Analysis of scRNA-seq data revealed that genes involved in Trp metabolism were expressed in almost all the cell types in glioblastoma and that most cell types, in particular macrophages and T cells, exhibited AHR activation. Moreover, high AHR activity associated with reduced overall survival in the glioblastoma TCGA dataset. Conclusion: The novel techniques we developed could support the identification of patients that may benefit from therapies targeting TCEs or AHR activation.

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“…This approach has also allowed deep proteome quantification from small cancer samples ( 35 ) and increased sensitivity of thermal proteome profiling ( 36 ). Using the TMTpro 18-plex reagents ( 37 ), multiplexed single-cell proteomics methods can quantify thousands of proteins across thousands of individual cells within weeks and thus generate single-cell data at a comparable scale to multiwell-based scRNA-Seq methods ( 38 ). A major difference from comparable scRNA-Seq methods is that multiplexed single-cell proteomics methods have not yet become as widely employed.…”

Section: Trade-offs Between Single-cell Proteomics Methodsmentioning

confidence: 99%

Scaling Up Single-Cell Proteomics

Slavov

2022

Molecular & Cellular Proteomics

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Single-cell tandem MS has enabled analyzing hundreds of single cells per day and quantifying thousands of proteins across the cells. The broad dissemination of these capabilities can empower the dissection of pathophysiological mechanisms in heterogeneous tissues. Key requirements for achieving this goal include robust protocols performed on widely accessible hardware, robust quality controls, community standards, and automated data analysis pipelines that can pinpoint analytical problems and facilitate their timely resolution. Toward meeting these requirements, this perspective outlines both existing resources and outstanding opportunities, such as parallelization, for catalyzing the wide dissemination of quantitative single-cell proteomics analysis that can be scaled up to tens of thousands of single cells. Indeed, simultaneous parallelization of the analysis of peptides and single cells is a promising approach for multiplicative increase in the speed of performing deep and quantitative single-cell proteomics. The community is ready to begin a virtuous cycle of increased adoption fueling the development of more technology and resources for single-cell proteomics that in turn drive broader adoption, scientific discoveries, and clinical applications.

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TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing

Cited by 197 publications

References 39 publications

Proteomic landscape of Alzheimer’s Disease: novel insights into pathogenesis and biomarker discovery

Proteomic landscape of Alzheimer’s Disease: novel insights into pathogenesis and biomarker discovery

Tryptophan metabolism is inversely regulated in the tumor and blood of patients with glioblastoma

Scaling Up Single-Cell Proteomics

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