The present invention generally provides, in various embodiments, improved methods of analyzing proteins utilizing liquid chromatography and tandem mass spectroscopy (LC-MS/MS), such as by multiplexing samples and using data-independent acquisition.

A precursor ion selection processing unit (22) sequentially selects precursor ions having different mass-to-charge ratios, and causes an MS/MS spectrum data acquisition processing unit (23) to acquire MS/MS spectrum data corresponding to each precursor ion. The precursor ion selection processing unit (22) sequentially selects the precursor ion having a mass-to-charge ratio which is not included in a predetermined range with respect to a mass-to-charge ratio of the precursor ion for which the MS/MS spectrum data has already been acquired.

A method of determining one or more interference parameters for a particular peak of an isotopic distribution corresponding to a precursor molecule in MS scan data is provided. The MS scan data comprises a plurality of peaks. Each peak has a mass-to-charge ratio and a relative abundance. The isotopic distribution comprises a subset of the plurality of peaks. The one or more interference parameters comprises a peak purity, p.sub.i, for the particular peak. The method comprises determining that there are no interfering peaks relevant to the isotopic distribution and determining that the peak purity, p.sub.i, for the particular peak should be a maximum purity value. Alternatively, the method comprises identifying one or more interfering peaks from the MS scan data, wherein the one or more interfering peaks do not belong to the subset of peaks of the isotopic distribution, and determining the peak purity, p.sub.i, for the particular peak based on: the relative abundance, I.sub.i, of the particular peak, and the relative abundance of the one or more interfering peaks.

A method of mass spectrometry is disclosed comprising: a step (10) of analysing a reference compound in a first mass spectrometer and outputting mass spectral data in response thereto; a step (20) of analysing the reference compound in a second, different mass spectrometer and outputting mass spectral data in response thereto; and a step (30) of automatically adjusting an operational parameter, duty cycle (e.g. duty cycle of data acquisition), or acquired spectral data of at least one mass spectrometer such that, for the same (given) consumption of reference compound by the spectrometer, the statistical precision of quantification (the number of detected ions) and/or of mass measurement (the mass resolution) by the mass spectrometer is substantially the same as that of the other mass spectrometer. A similar method of ion mobility spectrometry is disclosed.

Methods are described for measuring the amount of one or more of vitamin A, α-tocopherol, and the combination of β-tocopherol and γ-tocopherol in a sample. More specifically, mass spectrometric methods are described for detecting and quantifying one or more of vitamin A, α-tocopherol, and the combination of β-tocopherol and γ-tocopherol in a sample.

A first mass spectrum including a fragment ion peak is generated under application of a first ionization method. A second mass spectrum including a molecular ion peak is generated under application of a second ionization method. These mass spectra are synthesized to generate a synthesized mass spectrum. On the synthesized mass spectrum, difference information, such as a mass difference and difference composition, is calculated between the molecular ion peak and the fragment ion peak.

A method includes obtaining a first mass spectrum; selecting a first peak of the first mass spectrum; fragmenting and analyzing ions of the first peak to obtain a second mass spectrum; performing a real-time spectral search for compounds corresponding to peaks in the second mass spectrum; identifying fragments for the compounds identified based on the real-time spectral search; adding mass-to-charge ratios for the fragments to an exclusion list; selecting a second peak present in the first mass spectrum and not on the exclusion list; and fragmenting and analyzing ions of the second peak to obtain a third mass spectrum.

Before each sample of a series of batch samples is introduced into a liquid sample delivery device, an ion source device receives aqueous mobile phase solution from the liquid sample delivery device and ionizes its compounds, producing an ion beam. A tandem mass spectrometer performs a neutral loss or precursor ion scan on the ion beam to measure intensities of two or more precursor ions corresponding to a known aqueous mobile phase solution compound. Intensity measurements for each of the two or more different precursor ions are compared to previously stored intensities to determine the threshold times at which these measurements indicate orifice contamination. A threshold time is then predicted for a known compound of interest of the batch samples based on the m/z value of the known compound of interest and the m/z value and the threshold time of each of the two or more different precursor ions.

Methods are described for measuring the amount of one or more of vitamin A, α-tocopherol, and the combination of β-tocopherol and γ-tocopherol in a sample. More specifically, mass spectrometric methods are described for detecting and quantifying one or more of vitamin A, α-tocopherol, and the combination of β-tocopherol and γ-tocopherol in a sample.

The present invention generally pertains to methods of characterizing at least one protein of interest in a biological sample. In particular, the present invention pertains to the use of automated iterative tandem mass spectrometry (AIMS) to identify, quantify and characterize at least one protein of interest and/or biomarker from a biological sample such as plasma.