University of North Texas 
For the targeted metabolomics a scan survey called Multiple Reaction Monitoring (MRM) is used to detect and quantify metabolites by LC-MS/MS. On the other hand, full scan or Single Ion Monitoring (SIM) is performed when GC-MS is selected to analyze volatile compounds.
Amino Acids
Amino acids and their derivatives are analyzed using an Agilent 1290 Infinity II coupled to an ABSciex QTRAP 6500+ LC-MS/MS system. The analytical method is described in a peer-review paper published by Cocuron et al. (2014). The run time is 10 minutes.
Microcystins
Microcystins are analyzed using an Agilent 1290 Infinity II coupled to an ABSciex QTRAP 6500+ LC-MS/MS system. The analytical method uses a BEH C18 (2.1 x 50 mm; 1.7 micron) column from Waters. The run time is 5 minutes.
Phenolics/Hormones/Secondary Compounds
Alkaloids, flavonoids, hormones, phenolics (acids, alcohol, aldehydes), and stilbenes are analyzed using an Agilent 1290 Infinity II coupled to an ABSciex QTRAP 6500+ LC-MS/MS system. The analytical method uses a Symmetry C18 (4.6 x 75 mm; 3.5 micron) column from Waters. The run time is 15 minutes.
Phosporylated Compounds and Organic Acids
Phosphorylated compounds and organic acids are quantified using an Agilent 1290 Infinity II coupled to an ABSciex QTRAP 6500+ LC-MS/MS system. The analytical method is described in two peer-review papers published by Alonso et al. (2010) and Koubaa et al. (2013). Note that organic acids can be separated in 60 minutes whereas phosphorylated compounds in 80 minutes.
Polyamines
Polyamines are analyzed using an Agilent 1290 Infinity II coupled to an ABSciex QTRAP 6500+ LC-MS/MS system. The analytical method utilizes a Zorbax Eclipse Plus C18, RRHD (2.1 x 50 mm; 1.8 micron) column from Agilent. The run time is 10 minutes.
Polyunsaturated Aldehydes
Polyunsaturated aldehydes are quantified using Thermo Trace 1310 Gas Chromatography Coupled to a Single Quadrupole Mass Spectrometer (ISQ) system. The analytical method uses a TG5-MS (30 m x 0.25 mm x 0.50 micron) column from ThermoFisher. The analytical method is described in two peer-review papers published by Lavrentyev et al. (2015). The run time is 30 minutes.
Sugars & Sugar Alcohols
Sugars and sugar alcohols are analyzed using an Agilent 1290 Infinity II coupled to an ABSciex QTRAP 6500+ LC-MS/MS system. The analytical method is described in a peer-review paper published by Cocuron et al. (2014). The run time is 20 minutes.
Others
The metabolites reported above are analyzed using an Agilent 1290 Infinity II coupled to an ABSciex QTRAP 6500+ LC-MS/MS system.