Thermo Finnigan LLC

Sebastien F Gallien

Philip M Remes

David A Sarracino

Aaron Gajadhar

A Liquid Chromatography Mass Spectrometry system comprises: a chromatograph; a mass spectrometer configured to ionize separated fractions of a sample received from the chromatograph; and a programmable processor operable to repeatedly execute the steps of: (i) causing the mass spectrometer to perform a data-independent analysis of the precursor ion species using a mass analyzer of the mass spectrometer; (ii) calculating one or more degree-of-matching scores that relate to detection of an internal standard; and (iii) if each of the degree-of-matching scores meets a respective degree-of-matching condition, performing a quantitative tandem mass spectrometric analyses of both the internal standard and the analyte; the programmable processor further operable to calculate a quantity of the analyte in the sample by comparison between intensities of one or more mass spectral signals generated by the quantitative tandem mass spectrometric analyses of the analyte and the internal standard.

Methods and apparatus for targeted mass spectral proteomic analyses

A method for determining a quantity of an analyte in a liquid sample, comprises: adding a known quantity of an internal standard comprising an isotopically labeled version of the analyte to the sample; (b) providing a continuous stream of the sample having the internal standard to an inlet of a Liquid Chromatography Mass Spectrometry (LCMS) system; and repeatedly performing the steps of: performing a data-independent analysis of the precursor ion species using a mass analyzer, whereby mass spectra of a plurality of fragment-ion species are acquired; calculating one or more degree-of-matching scores that relate to either a number of ions of the internal standard that overlap between results of the data-independent analysis and tabulated mass spectral data of the internal standard; and performing quantitative tandem mass spectrometric analyses of the internal standard and the analyte if each of the degree-of-matching scores meets a respective degree-of-matching condition.

A targeted quantitation system for mass spectrometry may acquire, while operating in a watch mode, a watch mode mass spectrum including mass peaks for ions produced from a plurality of internal standard variants added to a sample comprising a target analyte. Each internal standard variant included in the plurality of internal standard variants includes a unique isotopologue of the target analyte and is added to the sample in a unique amount. The targeted quantitation system may generate a calibration curve based on the watch mode mass spectrum. The targeted quantitation system may acquire, while operating in a quantitation mode, a quantitation mode mass spectrum including mass peaks for ions produced from the target analyte included in the sample. The targeted quantitation system may determine a concentration of the target analyte included in the sample based on the calibration curve and the second mass spectrum.

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Sebastien F Gallien