Mass Spectrometer With Bypass of a Fragmentation Device

A method of analyzing a sample, including a mixture of components, with an apparatus including:

• an ion source;
• a collision, fragmentation or reaction device;
• a bypass device disposed upstream of the collision, fragmentation or reaction device;
• and a mass analyzer, said method comprising:
• separating or partially separating different components of the mixture;
• providing a sequential eluent of the components to the ion source over a period of time, wherein the step of separating or partially separating is performed by liquid chromatography, High Performance Liquid Chromatography (“HPLC”), anion exchange, anion exchange chromatography, cation exchange, cation exchange chromatography, ion pair reversed-phase chromatography, chromatography, single-dimensional electrophoresis, multidimensional electrophoresis, size exclusion, affinity or reverse-phase chromatography, Capillary Electrophoresis Chromatography (“CEC”), electrophoresis, ion mobility separation, Field Asymmetric Ion Mobility Separation (“FAIMS”) or capillary electrophoresis;
• generating ions with the ion source;
• switching the bypass device to cause ions from the ion source to either pass through the collision, fragmentation or reaction device or bypass the collision, fragmentation or reaction device;
• and
• obtaining mass spectra from ions received from the collision, fragmentation or reaction device and from ions that bypassed the collision, fragmentation or reaction device.