Data integration and analysis. Standards for benchmarking quantification | Nikolai Slavov | SCP2019 скачать в хорошем качестве

Data integration and analysis. Standards for benchmarking quantification | Nikolai Slavov | SCP2019

Presentation by Nikolai Slavov at the second single-cell proteomics conference https://single-cell.net. A playlist of all workshop videos: http://workshop2019.single-cell.net. More information & videos: https://slavovlab.net & http://youtube.slavovlab.net I will discuss our efforts and progress on miniaturizing and automating sample preparation for single-cell proteomics, with special emphasis on key challenges and the solutions that enabled us to increase the quality of our data and the throughput of our analysis. I will present single-cell protein measurements from monocytes differentiating to macrophages in the context of many standards and benchmarks that give us confidence in the data. Some of the benchmarks suggest that single-cell protein measurements by mass-spec can be much more accurate than single-cell RNA measurements by RNA-seq. The last part of the talk will be devoted to community standards that I believe are essential for the healthy growth of this emerging field. Many of these standards relate to data analysis, so I will share approaches that have proven useful to us and ideas for future approaches that I believe will transform our understanding of biological systems. Relevant publications for further reading: Specht H, Emmott E, Koller T, Slavov N (2019) High-throughput single-cell proteomics quantifies the emergence of macrophage heterogeneity, bioRxiv DOI: https://doi.org/10.1101/665307 Specht H, Harmange G, Perlman DH, Emmott E, Niziolek Z, Budnik B, Slavov N. (2018) Automated sample preparation for high-throughput single-cell proteomics bioRxiv DOI: http://dx.doi.org/10.1101/399774 Huffman RG, Specht H, Chen AT, Slavov N. (2019) DO-MS: Data-Driven Optimization of Mass Spectrometry Methods J. of Proteome Res. DOI: https://doi.org/10.1021/acs.jproteome... Chen AT, Franks A, Slavov N. (2019) DART-ID increases single-cell proteome coverage PLoS Computational Biology DOI: https://doi.org/10.1371/journal.pcbi.... Specht H, and Slavov N. (2018) Transformative opportunities for single cell proteomics Journal of Proteome Research DOI: https://doi.org/10.1021/acs.jproteome... Budnik B., Levy E., Harmange G., Slavov N. (2018) SCoPE-MS: mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation Genome Biology DOI: https://doi.org/10.1186/s13059-018-15...