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Open Access Small Molecule Analysis
The facility specializes in offering an ‘Open Access’ format for many users. This format is based on a combination of specific software and the use of autosamplers for sample introduction. Instruments in this format are available on a 24/7 basis. Open Access instruments include:
  • ESI-TOF-MS (1 instrument open access; 1 instrument staff operated) in flow injection mode (FIA): Waters LCTs
  • ESI-TOF-MS with reversed phase LC (columns: C4, C18, PFP, custom): Xevo G2-XS and Synapt G2s)
  • ESI-QDA-MS (3 instruments) with reversed phase or HILIC LC: Acquity-QDAs, Acquity-Quattro Premier
  • GC-MS (4 instruments) with EI and CI (ammonia reagent gas): Waters GCT (TOF), Thermo UltraRSH and ISQD, Agilent GC-MS/FID w/Markers TD
  • MALDI-TOF/TOF (2 instruments) AB Sciex 5800 and Bruker ultrafleXtreme for IMS
Small molecule sample preparation – polar molecules:
Polar molecules are analyzed using ESI (usually one or two heteroatoms are sufficient to obtain an adequate response)
Approximately the amount used in a TLC analysis can be used to prepare an ESI sample.
For FIA the sample should be dissolved in methanol in a 7 x 40 mm ‘mass spec’ vial. We recommend obtaining a bag of vials from PS stores and a bottle of high purity methanol (Fisher Optima LC-MS grade (not ACS or HPLC grade !)
For LC-MS, the standard sample buffer is 90% water:10% acetonitrile. For less polar compounds (e.g. lipids), you can increase the percentage of acetonitrile to 20-30 % but do not exceed 50%.
ESI results:
For the most part ESI generates molecular weight information usually as [M + Na]+, i.e., a sodiated ion. Other ions may also occur including [M + H]+, [M + NH4]+, [M + K]+
Small molecule sample preparation – non-polar molecules:
Non-polar molecules are analyzed using GC-MS (‘one polar group good, two polar groups or more bad and don’t run acids’ is a reasonable indicator of when GC-MS is applicable with –OH and NH2 as the relevant polar groups).
Samples should be dissolved in a non-polar solvent, e.g., alkanes, ether, benzene, dichloromethane, chloroform or ethyl acetate. The preferred solvent is dichloromethane (DCM). Do NOT use acetonitrile, any alcohol, or water.
Sample concentration should be about 5-50µg/mL (50-500 µM). This is pretty concentrated but usually is a good starting point.
GC-MS results:
EI (electron ionization) is an energetic process that uses a beam of 70 eV electrons that causes extensive fragmentation of the analyte even to the point that the molecular ion may not be observed. When seen the molecular ion occurs as [M]+, i.e. the molecular weight of the ion without any adducted species.
CI (chemical ionization). We use ammonia as the reagent gas so ions formed are typically [M + H]+ or [M + NH4]+ with minimal fragmentation.