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SCOPE-MS Extensions


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:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1547-5

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:

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
    • SILAC
    • Label-free/iBAQ
  • 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 R, python, and MATLAB.

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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