| Author | Martins, Aline M. A. | |
| Author | Santos, Marlon D. M. | |
| Author | Camillo-Andrade, Amanda C. | |
| Author | Leite, Aline Lima | |
| Author | Souza, Janaina Sena | |
| Author | Sánchez, Sandra | |
| Author | Muotri, Alysson R. | |
| Author | Carvalho, Paulo Costa | |
| Author | Yates III, John R. | |
| Access date | 2024-12-23T23:59:14Z | |
| Available date | 2024-12-23T23:59:14Z | |
| Document date | 2024 | |
| Citation | MARTINS, Aline M. A. et al. Integrating DIA single-cell proteomics data with the DiagnoMass proteomic hub for biological insights. Journal of the American Society for Mass Spectrometry, v. 35, p. 2308-2314, 2024. | en_US |
| ISSN | 1879-1123 | en_US |
| URI | https://www.arca.fiocruz.br/handle/icict/67772 | |
| Description | The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jasms.4c00187. | en_US |
| Sponsorship | P.C.C., M.D.M.S., and A.C.C.A. received funding from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), the Fiocruz Inova initiative, and the Fundação Araucaria. ́ Funding was provided by National Institutes of Health to J.R.Y.: R21129776 and R01MH100175. | en_US |
| Language | eng | en_US |
| Publisher | ACS Publications | en_US |
| Rights | restricted access | |
| Subject in Portuguese | Aquisição independente de dados | en_US |
| Subject in Portuguese | Organoides cerebrais | en_US |
| Subject in Portuguese | Espectrometria de massas | en_US |
| Subject in Portuguese | Síndrome de Rett | en_US |
| Title | Integrating DIA single-cell proteomics data with the DiagnoMass proteomic hub for biological insights | en_US |
| Type | Article | |
| DOI | 10.1021/jasms.4c00187 | |
| Abstract | Single-cell proteomics has emerged as a powerful technology for unraveling the complexities of cellular heterogeneity, enabling insights into individual cell functions and pathologies. One of the primary challenges in single-cell proteomics is data generation, where low mass spectral signals often preclude the triggering of MS2 events. This challenge is addressed by Data Independent Acquisition (DIA), a data acquisition strategy that does not depend on peptide ion isotopic signatures to generate an MS2 event. In this study, we present data generated from the integration of DIA single-cell proteomics with a version of the DiagnoMass Proteomic Hub that was adapted to handle DIA data. DiagnoMass employs a hierarchical clustering methodology that enables the identification of tandem mass spectral clusters that are discriminative of biological conditions, thereby reducing the reliance on search engine biases for dentifications. Nevertheless, a search engine (in this work, DIA-NN) can be integrated with DiagnoMass for spectral annotation. We used single-cell proteomic data from iPSC-derived neuroprogenitor cell cultures as a test study of this integrated approach. We were able to differentiate between control and Rett Syndrome patient cells to discern the proteomic variances potentially contributing to the disease’s pathology. Our research confirms that the DiagnoMass-DIA synergy significantly enhances the identification of discriminative proteomic signatures, highlighting critical biological variations such as the presence of unique spectra that could be related to Rett Syndrome pathology. | en_US |
| Affilliation | The Scripps Research Institute. Departments of Molecular Medicine and Neurobiology. La Jolla, California, United States. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil / Institut Pasteur de Montevideo. Instituto de Investigaciones Biológicas Clemente Estable. Analytical Biochemistry and Proteomics Unit. Montevideo, Uruguay. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil | en_US |
| Affilliation | Bruker Daltonics Corporation. Billerica, Massachusetts, United States. | en_US |
| Affilliation | Sanford Consortium for Regenerative Medicine. Department of Pediatrics. La Jolla, California, United States. | en_US |
| Affilliation | Sanford Consortium for Regenerative Medicine. Department of Pediatrics. La Jolla, California, United States. | en_US |
| Affilliation | Sanford Consortium for Regenerative Medicine. Department of Pediatrics. La Jolla, California, United States. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. | en_US |
| Affilliation | The Scripps Research Institute. Departments of Molecular Medicine and Neurobiology. La Jolla, California, United States. | en_US |
| Subject | Data Independent Acquisition | en_US |
| Subject | DiagnoMass | en_US |
| Subject | Single-cell proteomics | en_US |
| Subject | Brain organoids | en_US |
| Subject | Rett syndrome | en_US |
| Subject | Mass spectrometry | en_US |
| DeCS | Espectrometria de Massas | en_US |
| DeCS | Síndrome de Rett | en_US |
| DeCS | Proteômica | en_US |
| Embargo date | 2034 | |
