Method and system for the identification of compounds in complex biological or environmental samples by receiving (102) a mass spectrum (1) from a mass spectrometry coupled with a separation technique; for each data point (2) of the mass spectrum (1), annotating (106) in an annotation database (12) combinations of formulas and adducts the theoretical mass-to-charge ratio of which (m/z).sup.T corresponds to the mass-to-charge ratio (m/z) measured of the data point (2); for each formula and adduct annotated, detecting (108) regions of interest in a retention time range (RT.sub.0-RT.sub.1) according to characterisation criteria; generating (110) an inclusion list (14) with the retention time ranges (RT.sub.0-RT.sub.1) and the theoretical mass-to-charge ratios (m/z).sup.T of the formulas and adducts associated with the regions of interest; and sending (112) the inclusion list to a mass spectrometer for the identification of compounds in the sample by tandem mass spectrometry.

In a general aspect, a swab sample is analyzed, for example, to test for disease. In some examples, a swab head of a swab sample is inserted through an opening into an internal reservoir of a sampling device. The sampling device includes the opening, an inlet channel, an outlet channel, and the internal reservoir. The internal reservoir is in fluid communication with the inlet channel, the outlet channel, and the opening. A liquid solvent is supplied to the swab head in the internal reservoir via the inlet channel of the sampling device. The swab head is held in the liquid solvent for a period of time to form an analyte in the internal reservoir. The analyte is extracted from the internal reservoir via the outlet channel of the sampling device. The analyte is transferred to and processed by a mass spectrometer to obtain mass spectrometry data.

An apparatus for analysing ions, including a first mass analyser configured to eject groups of ions in a predetermined sequence during different time windows; an ion transport device having a plurality of electrodes arranged around a transport channel; control means configured to control voltages applied to the electrodes to generate a transport potential in a transport channel, the transport potential having a plurality of potential wells configured to move along the transport channel such that each group of ions received by the ion transport device is respectively transported along the transport channel by one or more selected potential; fragmentation means configured to fragment precursor ions in each group of ions so as to produce product ions; and a second mass analyser configured to produce a respective mass spectrum using each group of ions after the group of ions has been fragmented and transported.

In order to suppress a charge-up in an ion source configured to ionize a component contained in a sample gas, a mass spectrometer according to the present invention is provided with an ion source (3) including: an ionization chamber (30) having an ion ejection opening (301) and internally having a space substantially separated from an outside area; a repeller electrode (31), located within the ionization chamber, for creating an expelling electric field which acts on an ion generated within the ionization chamber to expel the ion through the ion ejection opening to the outside area; and a voltage generator (7) configured to selectively apply, to the repeller electrode, a first voltage for creating the expelling electric field and a second voltage for creating a charge-up-removing electric field, where the second voltage is a positive voltage having a larger absolute value than the first voltage.

Techniques for real-time or substantially real-time peak detection are described. In one embodiment, for example, logic coupled to memory may be configured to receive data from at least one analytical instrument and perform processing or analysis on the received data. Moreover, the logic may be configured to determine, via one or more GPUs or CPUs (or both), one or more peaks based on the processing or the analysis of the received data and generate peak detection data based on the detected one or more peaks in real-time or substantially real-time. Other embodiments are described.

A mass spectrometry (MS) apparatus is provided. The MS apparatus includes a mass spectrometer, an ionization source coupled to the mass spectrometer, and a flow injection system (FIS) coupled to the ionization source. The ionization source is configured to provide an ionized gas flow of an analyte towards an entrance of the mass spectrometer. The ionization source is further configured to provide a second gas flow of a second gas. The MS apparatus is configured to measure a mass spectrometer (MS) signal of the analyte. The MS apparatus is further configured to analyze a dependency of the MS signal of the analyte versus a parameter of the second gas flow or a state of the second gas flow and to determine a condition of the apparatus based on the analyzed dependency.

Provided are methods of detecting the presence or amount of a vitamin D metabolite in a sample using mass spectrometry. The methods generally directed to ionizing a vitamin D metabolite in a sample and detecting the amount of the ion to determine the presence or amount of the vitamin D metabolite in the sample. Also provided are methods to detect the presence or amount of two or more vitamin D metabolites in a single assay.

Provided are methods of detecting the presence or amount of a vitamin D metabolite in a sample using mass spectrometry. The methods generally directed to ionizing a vitamin D metabolite in a sample and detecting the amount of the ion to determine the presence or amount of the vitamin D metabolite in the sample. Also provided are methods to detect the presence or amount of two or more vitamin D metabolites in a single assay.

A mass spectrometry method comprises: storing a first packet of ions within an ion storage apparatus; transferring the first ion packet into an electrostatic trap mass analyzer through a set of electrostatic lenses, wherein, during the transfer, either the lenses are operated in a first mode of operation or an injection voltage of a first pre-determined magnitude is applied to an electrode of the mass analyzer; mass analyzing the first ion packet using the mass analyzer; storing a second packet of ions within the ion storage apparatus; transferring the second ion packet into the mass analyzer through the set of lenses, wherein, during the transfer, either the lenses are operated in a second mode of operation or an injection voltage of a second pre-determined magnitude is applied to the electrode of the mass analyzer; and mass analyzing the second packet of ions using the electrostatic trap mass analyzer.

The disclosure relates to a method of operating a secondary-electron multiplier in the ion detector of a mass spectrometer so as to prolong the service life, wherein the secondary-electron multiplier is supplied with an operating voltage in such a way that an amplification of less than 10.sup.6 secondary electrons per impinging ion results, while the output current of the secondary-electron multiplier is amplified using an electronic preamplifier mounted close to the secondary-electron multiplier with such a low noise level that the current pulses of individual ions impinging on the ion detector are detected above the noise at the input of a digitizing unit. Further disclosed are the use of the methods for imaging mass spectrometric analysis of a thin tissue section or mass spectrometric high-throughput analysis/massive-parallel analysis, and a time-of-flight mass spectrometer whose control unit is programmed to execute such methods.