SCoPE-MS is a proteomics method that allows for the analysis of single mammalian cells by mass spectrometry. Read the open-access article here, in Genome Biology:
I joined the Slavov Lab in the middle of the development of SCoPE-MS, and was able to contribute by developing the last part of the quantitation pipeline – normalizing and filtering our data from MaxQuant so that it could be used for downstream biological analyses. I also helped clean up our core MATLAB processing code.
My more recent work with SCoPE-MS has been leading a project that applies its concepts to other areas of proteomics. For me this involves:
- Mammalian cell culture, mainly on blood cancer cell lines Jurkat (T-cells) and U-937 (monocytes)
- Proteomics sample preparation:
- mPOP cell lysis protocols – available here on bioRXiV
Figure 1. from Specht et al 2018
- Experimental cell lysis protocols
- Conventional and experimental protein digestions
- Various cleanup procedures, such as with C18 StageTips or SPE with Waters SepPaks
- Labeling, and optimizing labeling, with Thermo tandem-mass-tags (TMT)
- Running a variety of MS quantitation methods
- Isobaric-tag, TMT
- Optimizing LC-MS parameters
- Current system is with a Dionex LC, and a base model Q-Exactive.
- Front end/chromatography is changing frequently, but it’s usually a standard reverse phase, nano-LC column, with a fused ESI spray tip and an ABIRD in the source.
Our lab’s setup with a shrine to Alexander Makarov, inventor of the Orbitrap analyzer
In addition to running physical experiments I am writing software tools to help process our data. These are written in a mix of
Recently, much of our analysis has been offloaded/automated with the DO-MS application, which I encourage you to check out! It eliminates the process of creating scripts for each individual experiment, and allows me to quickly share reports with my colleagues.
Stay tuned! Data/methods will be posted as soon as they are ready.
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