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Laboratory protocols used by the Metabolite Chemistry Analysis Center, a ChEM-H Knowledge Center at Stanford University.
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Stanford ChEM-H MCAC Protocols

This repository contains laboratory protocols for operating mass spectrometers in Stanford's ChEM-H Metabolic Chemistry Analysis Center. The protocols are formatted in markdown (*.md) format for easy manipulation and pretty display on GitHub.


Protocols are loosely organized into sub-directories.

  1. The two most commonly used protocols -- for starting runs -- are in the root directory:

  2. instrument_maintenace_and_configuration is a subdirectory for protocols on periodic maintenance, instrument reconfiguration, column cleaning, the composition of the tuning mix etc.

  3. sample_preparation is a subdir for prepping samples.

  4. changing_ion_sources is a subdir for how to swap out one ion source (e.g. dual AJS) for another (e.g. MMI).

  5. installation is a subdir containing tales of woe and caution related to the installation of mass spectrometers.

  6. software is a subdir containing protocols for how to set up metabolomics software on your own local computer.

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