Mass Spectrometry Facility – Services

Walk-up APCI LC-MS

Users may analyze samples any time of the day or night using our Agilent 1100 LC-MSD VL quadrupole instrument once they have completed the training course. The instrument is equipped with an atmospheric pressure chemical ionization (APCI) source, which is capable of ionizing a broad range of compounds. The instrument is set up to perform a two minute isocratic run through a short C18 column. Users may select positive or negative ion analysis as well as varying the amount of sample loaded and the m/z range analyzed. This configuration allows quick and easy analysis of reaction products to accelerate drug discovery and other research at UW.


Liquid chromatography is a powerful technique for analyzing complex mixtures. Detection of compounds in mass spectrometry relies on the ability to ionize target compounds. In complex mixtures low abundance compounds or those that are difficult to ionize may be masked by higher abundance, easily ionized compounds. This type of interference is referred to as “suppression”. Supression effects can be reduced or eliminated by separating the compounds to be analyzed before they are introduced into the mass spectrometer. We have an Agilent 1100 LC-MSD quadrupole SL instrument that we can easily re-configure with a variety of columns and solvent systems to screen various biological matrices for compounds of interest. We also frequently use this instrument for quantitation of drugs and drug metabolites in plasma, serum extracts or other bio-fluids.

MSn for Structural Analysis

The structure of a compound can be deduced by fragmenting the parent ion and measuring the masses of the fragment ions. The AIC MS facility has an 1100 MSD Trap SL instrument with which we can iteratively isolate a parent ion and measure the masses of fragments produced by collision induced dissociation (CID). Thus we can sequentially break the parent compound into smaller and smaller pieces to learn about its structure.

Accurate Mass Analysis

When characterizing novel compounds a mass measurement with sufficient resolution and mass accuracy can be used to generate a molecular formula. At the AIC MS facility we have an IonSpec ProMALDI Fourier transform ion cyclotron resonance (FTICR) mass spectrometer which is capable of mass measurements with sub-ppm mass accuracy and resolution (FWHM) in the range of 60,000. This is sufficient for assigning formulae for most compounds up to ~500 Da. Our ProMALDI also has MS/MS capabilities for structural determination using SORI-CID in the cell.