April 3, 2019 MIA Meeting: https://www.youtube.com/watch?v=P0-_g…
Nikolai Slavov Northeastern Bioengineering Understanding biological systems: In search of direct causal mechanisms
Abstract: The advent of DNA-microarrays spurred a vigorous effort to reverse engineer biological networks. Recently, these efforts have been reinvigorated by the availability of RNA-seq data from perturbed and unperturbed single cells. I will discuss the opportunities and limitations of using such data for inferring networks of direct causal interactions, with emphasis on the distinctions between models based on direct and indirect interactions. This discussion motivates the need to model proteins since most biological interactions involve proteins. Then I will introduce key ideas and technological capabilities of high-throughput single-cell proteomics methods that we have developed and will focus on the opportunities of using such data for inferring direct causal mechanisms in biological systems. Harrison Specht Slavov Lab, Northeastern Bioengineering Primer: Quantifying proteins by mass-spec Abstract: Mass spectrometry-based proteomics is a suite of high-throughput and sensitive approaches for identifying and quantifying proteins in biological samples. These methods allow for quantifying greater than 10,000 proteins in bulk samples. However, these techniques have not yet been widely applied to single cells despite the fact that modern mass spectrometers can detect single ions. To explain why, this primer talk will explore core concepts of mass spectrometry-based proteomics with emphasis on developing intuition for the physical processes underpinning peptide sequencing and quantification. In particular, I will cover what is called “shotgun” or “discovery” proteomics using isobaric barcoding, a technology used by Single Cell Proteomics by Mass Spectrometry (SCoPE-MS). The primer talk will outline the obstacles that have limited the broad application of quantitative mass spectrometry to single-cell analysis and how SCoPE-MS overcomes these obstacles to enable profiling thousands of proteins across thousands of single cells.
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