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.

Organization

Protocols are loosely organized into sub-directories.

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

   • start_6545_lcms_run_protocol. This protocol is the most often used document in the repository.
   • start_6470_lcms_run_protocol is the companion protocol for the 6470 QQQ MS is

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.