The invention generally relates to systems and methods for precursor and neutral loss scan in an ion trap. In certain aspects, the invention provides a system that includes a mass spectrometer having an ion trap, and a central processing unit (CPU). The CPU includes storage coupled to the CPU for storing instructions that when executed by the CPU cause the system to excite a precursor ion and eject a product ion in the single ion trap.

The invention generally relates to systems and methods for performing multiple precursor, neutral loss and product ion scans in a single ion trap. In certain aspects, the invention provides systems including a mass spectrometer having a single ion trap, and a central processing unit (CPU), and storage coupled to the CPU for storing instructions that when executed by the CPU cause the system to apply at least one of the following ion scans to a single ion population in the single ion trap: multiple precursor ion scans, a plurality of segmented neutral loss scans, or multiple simultaneous neutral loss scans.

Provided are methods for determining the amount of reverse T3 in a sample using mass spectrometry. The methods generally involve ionizing reverse T3 in a sample and detecting and quantifying the amount of the ion to determine the amount of reverse T3 in the sample.

A method of tandem mass spectrometry for analysing precursor ions across a mass to charge (m/z) range of interest is provided. The method comprises analysing some of the precursor ions across the m/z range of interest in the MS1 domain using a first mass analyser of a tandem mass spectrometer operated at a first sensitivity. The method also comprises analysing some of the precursor ions across the m/z range of interest in the MS1 domain using a second mass analyser of the tandem mass spectrometer operated at a second sensitivity, wherein the second sensitivity is higher than the first sensitivity. The analysis in the MS1 domain performed by the second mass analyser is performed concurrently with the analysis performed in the MS1 domain by the first mass analyser. The method also comprises combining data from the MS1 analyses performed by the first and second mass analysers to identify and/or quantify precursor ions. The method also comprises analysing some of the precursor ions in the MS2 domain using the second mass analyser of the tandem mass spectrometer.

The invention generally relates to systems and methods for conducting neutral loss scans in a single ion trap. In certain aspects, the invention provides systems that include a mass spectrometer having a single ion trap, and a central processing unit (CPU), and storage coupled to the CPU for storing instructions that when executed by the CPU cause the system to apply a scan function that excites a precursor ion, rejects the precursor ion after its excitation, and ejects a product ion in the single ion trap.

A method of quantitative mass analysis of precursor ion species of different mass-to-charge (m/z) ratios from the same or common ion injection event is disclosed. A plurality of precursor ion species with different respective m/z ratios are introduced into an ion trap mass analyzer at the same time. The precursor ion species are isolated. A first subset of the isolated precursor ions, which are multiply charged and have a first m/z ratio range, is fragmented and scanned by dividing the scan into at least two separate scan windows. A first mass spectrum is generated for the fragment ions of the first subset of precursor ions. A second subset of the isolated precursor ions having a second m/z ratio is fragmented and scanned, and a second mass spectrum is generated for the fragment ions of the second subset of precursor ions.

Provided are methods for determining the amount of reverse T3 in a sample using mass spectrometry. The methods generally involve ionizing reverse T3 in a sample and detecting and quantifying the amount of the ion to determine the amount of reverse T3 in the sample.

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.

A data independent acquisition method of mass spectrometry for analysing a sample as it elutes from a chromatography system is disclosed. The method comprises the steps of: ionising the sample to produce precursor ions, selecting a precursor mass range for the sample to be analysed, performing a plurality of MS1 scans and performing at most two sets of MS2 scans. Each of the MS1 scans uses a mass analyser operated at a first, relatively higher resolution, for identification and/or quantitation of the sample in the MS1 domain across the precursor mass range. The set of MS2 scans comprises performing MS2 scans of fragmented mass range segments performed with the mass analyser, operated at a second, relatively lower resolution. In the method, the MS1 scans are interleaved throughout the performing of the set of MS2 scans such that the MS1 scans provide a mass chromatogram of the sample.

A method and apparatus for improving the quality of spectra of a sample obtained from a tandem mass spectrometer system containing an ion trap. The method and apparatus includes the setting of an upper and lower threshold limit on peak intensity and only triggering an enhanced product ion scan when a detected intensity of a peak in an initial scan falls between the upper and lower threshold limits. The spectra obtained from an enhanced product ion scan conducted in this manner are useful in library matching of spectra. The ion trap may be a linear ion trap and the sample may be a peptide.