A method of analyzing data from a mass spectrometer for a data dependent acquisition is described. In an embodiment of this method, mass spectral scans are taken of a sample eluted from a liquid chromatography column. An extracted ion chromatogram (XIC) is then created for each m/z data point of the mass spectral scans and the XIC for each m/z data point are correlated to a model function, such as a monotonically increasing function, or the first half of a gaussian function, to obtain a XIC corr...

A mass spectrometer and a method of mass spectrometry are disclosed wherein periodic background noise is effectively filtered out from the mass spectral data. An overall mass window is superimposed upon the mass spectral data. The overall mass window preferably comprises 21 nominal mass windows each preferably having a width of 1.0005 amu. Each nominal mass window preferably comprises 20 channels. An intensity distribution relating to all the first channels of the 21 nominal mass windows is dete...

The invention provides, in various embodiments, systems and methods relating to controlling ion behavior in an ion-based analysis system.

In a mass spectrometer, an ion of a sample gas is produced in an ion source by colliding the gas with an electron beam, and is introduced into a magnetic field or an electric field. The ion is separated based on the mass number, and the sample is analyzed from a mass spectrum. The ion source has an electrode made of stainless steel, which is baked at a temperature in a range from 200.degree. C. to 700.degree. C. in an air atmosphere.

Method and apparatus, including computer program products, implement techniques for operating a mass spectrometer that includes a source of ions, a mass analyzer, and a detector, in which a gain of the detector or the number of ions detected by the detector is calculated based on intensity measurements for ions having a plurality of different m/z values. In particular implementations, the detector gain or the number of ions detected by the detector can be calculated based on a ratio of or differ...

A first mass spectrum and a second mass spectrum of the same ion sample can be analyzed to determine reaction pairs. These reaction pairs are determined based on a selected neutral difference by shifting the second mass spectrum by the neutral difference relative to the first mass spectrum to provide a shifted mass spectrum. Then, the shifted mass spectrum is compared with the first mass spectrum of the ion sample to determine the reaction pairs based on the neutral difference.

A mass spectrometry system is described. The mass spectrometry system comprises: (a) a mass spectrometer; and (b) a controller connected to the mass spectrometer. The controller is configured to: (i) direct the mass spectrometer to acquire a precursor ion spectrum of a sample stream; (ii) analyze, in real-time, the precursor ion spectrum to determine whether a first evaluation criterion is satisfied; (iii) if the first evaluation criterion is satisfied, direct the mass spectrometer to acquire a ...

Processes and apparatus are described for the analysis of molecules or fragments thereof, which are capable of carrying multiple charges, by reacting the multiply charged molecules or fragments thereof with other ions using mass spectrometry.

The invention provides methods and apparatus for tandem mass spectrometry (MS/MS) in which parent ions generated from a sample are passed through a mass filter (2) and are fragmented into daughter ions in fragmentation means (3), the daughter ions being passed through a discontinuous output mass analyser, such as a time-of-flight analyzer (16) or an ion storage device (29). The range of possible parent mass-to-charge ratios is split into a plurality of smaller ranges, and the mass filter (2) is ...

A method of managing the data for a plurality of ion spectra, including at least one progenitor ion spectrum and a plurality of spectra of ion fragments that are descendants of the progenitor ion, stored in a memory includes displaying indicia of the spectra on a display screen in a graphical user interface such that descendant ions have indicia that are displayed as subordinate to indicia of their progenitor ions, and manipulating the spectra data by selection of the displayed indicia with a gr...