Analytical instruments in general have variations in their capabilities as a result of their individual design and intended purpose. Mass analyzers also have their variations their strengths and weaknesses associated with each variation. A mass analyzer measures gas phase ions with respect to their (m/z). It is important to remember that mass analyzers measure m/z ratio, not mass. Quadrupoles and TOFs separate ions in space. Ion trap separates ions in time.

Mass Analyzers	Detection Method
Quadrupole	Scan radio frequency field (RF)
Quadrupole ion trap	Scan radio frequency field (RF)
TOF	TOF correlated directly to ion’s m/z
TOF Reflectron	TOF correlated directly to ion’s m/z
Quad-TOF	RF scanning + TOF
FT-ICR	Translates ion cyclotron motion to m/z

Mass Analysis

Performance characteristics: The performance of a mass analyzer is judged by accuracy, resolution, mass range, tandem analysis capabilities, and scan speed.

Accuracy: The ability with which the analyzer can accurately provide m/z information. This is largely a function of an instrument’s stability and resolution.

Resolution: The ability of a mass spectrometer to distinguish between ions of different m/z ratios. So, greater resolution means increased ability to differentiate ions. As the data acquisition rate decreases, the resolution decreases as well.

Mass Range: The m/z range of the mass analyzer.

Tandem Mass Analysis: The ability of the analyzer to separate different molecular ions, generate fragment ions from a selected ion, and then measure the mass of fragmented ions. Fragmented ions are used for structural determination.

Scan speed: This refers to the rate at which the analyzer scans over a particular mass range.

Sensitivity: Sensitivity is an absolute quantity; resolution is a relative quantity. Sensitivity describes the smallest absolute amount of change that can be detected by a measurement. Sensitivity should not be confused with accuracy—they are entirely different parameters.

Purity: How well you can separate complex mixtures.

Cleanliness: Eliminate molecules that interfere with ionization/detection.

Isotopes: Isotopes are forms of an element whose nuclei have the same atomic number - the number of protons in the nucleus - but different mass numbers because they contain different numbers of neutrons. Isotopes have the same charge but different mass.

Charge-based data acquisition

Mass spectrometers can be made to record either positive or negative ions by making the source voltage positive or negative.

• Peptides are best analyzed as positive ions

• Phosphorylated or sulphated peptides may be analyzed in negative ion mode
• Fatty acids are best analyzed as fatty acyl anions
• Carbohydrates are more easily protonated than deprotonated
  

Tandem Analysis

Space vs. Time

Tandem is space refers to precursor selection, dissociation, and fragment separation taking place in different compartments of the mass spectrometer. e.g. TOF/TOF, QTOF, 3Q, etc.

Tandem is time refers to precursor selection, dissociation, and fragment separation taking place in the same space but at different times. e.g. ion trap, FT-ICR.