A mass spectrometer including chromatogram creation means for creating a chromatogram showing changes over time in an ion intensity within a predetermined mass range based on the MS analysis results, and timing determination means for determining a timing to perform MS/MS analysis based on the chromatogram. The timing determination means determines, as a timing to perform MS/MS analysis, a point in time at which a signal intensity in the chromatogram reaches a predetermined upper limit after exceeding a predetermined lower limit or a point in time at which a signal intensity in the chromatogram reaches a top of a peak without reaching the upper limit after exceeding the lower limit. It is thus possible to collect precursor ions at a timing at which the signal intensity of a peak originating from sample components is highest between the upper limit and lower limit, thereby obtaining a high quality MS/MS spectrum.

The present invention relates to assays and methods for the detection of transthyretin and its isoforms. Specifically, the assays and methods of the present invention embrace liquid chromatography and mass spectrometry. The present invention also relates to unique peptides and peptide variants useful in the assays and methods.

A method of mass spectrometry is disclosed comprising passing ions through a first stage and a second stage of a mass spectrometer and monitoring a first ion acquisition for a first dwell time extending from a time T.sub.1 to a time T.sub.1+T.sub.dwell1. The method further comprises reconfiguring the mass spectrometer or one or more components of the mass spectrometer to monitor a second ion acquisition and setting the first stage to transmit ions of the second ion acquisition at a time T, wherein T<T.sub.1+T.sub.dwell1. The method further comprises monitoring the second ion acquisition for a second dwell time starting at a time T.sub.2, wherein T.sub.2>T.sub.1+T.sub.dwell1 and determining the time T based on a known or calculated ion transit time through one or more regions or components of the mass spectrometer disposed downstream of the first stage

Systems and methods are provided for scheduled MS.sup.3. A compound of interest is separated from a sample over a known time period using a separation device. A plurality of sMRM experiments are performed over the known time period on the separating compound of interest using a mass spectrometer. An intensity of a product ion of the compound of interest is produced for each of the plurality of sMRM experiments. Each intensity for the product ion for each of the plurality of sMRM experiments is compared to a threshold intensity level using a processor. When an intensity for the product ion of an sMRM experiment of the plurality of sMRM experiments is equal to or exceeds the threshold intensity level, the mass spectrometer is instructed to perform one or more MS.sup.3 experiments for the product ion using the processor.

Each sample of a series of samples is ejected at an ejection time and according to a sample order. Each ejected sample of the series is ionized, producing ion beam. A list of different sets of MRM transitions is received. Each set of the list corresponds to a different sample. A group of one or more different sets is selected from the list. Initially, each set selected for the group corresponds to a different sample of one or more first samples of the series. A mass spectrometer is instructed to execute each transition of each set of the group on the ion beam until a transition of a set of the group is detected, upon which, one or more next sets are selected from the list to be monitored using the set of the detected transition and the sample order.

First, an MS scan of a mass range of a control sample that does not include a metabolite is performed (601) producing background peak m/z and intensity values for background precursor ions (602). Background peaks are selected for an exclusion list and in the exclusion list an m/z value and an intensity value are included for each background peak (604). Next, an MS scan of the mass range of an experimental sample that does include a metabolite is performed (610) producing peak m/z and intensity values for precursor ions (612). Peaks are selected for a peak list and in the peak list an m/z value and an intensity value are included for each peak (614). Finally, each peak of the peak list that has both an m/z value and an intensity value that correspond to an m/z value and an intensity value of a background peak of the exclusion list is excluded from the peak list (616).