The invention generally relates to two-dimensional mass spectrometry using ion micropacket detection. In certain aspects, the invention provides systems including a mass spectrometer having an ion trap and one or more detectors. The system includes 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 one or more scan functions to the ion trap that excite a precursor ion and eject a product ion from the ion trap; and determine a secular frequency of the product ion by detecting micropackets of the product ion as the micropackets are ejected from the ion trap.

An apparatus for monitoring a surgical procedure includes a MALDI-TOF mass spectrometer comprising a load lock, an ionization chamber, and an ion detector. A first video camera produces an optical image of an operating field of the surgical procedure. A sample extracting device extracts the tissue sample at the location within the optical image of the operating field. A sample preparation system prepares MALID-TOF samples by depositing an extract of the extracted tissue sample on a sample plate together with a MALDI matrix. A sample plate loading mechanism loads the sample plate into the MALDI-TOF mass spectrometer. A second video camera produces an optical image of the sample plate and records a location of the extracted tissue sample. A computer records the images from first and second video cameras, correlates the location of the tissue sample in the operating field with the location of the tissue sample on the sample plate, acquires mass spectra data from the MALDI-TOF mass spectrometer, and compares the mass spectrum data to known mass spectrum data.

A method of processing data determined from an image-charge/current signal representative of ions of a given charge state (Q) undergoing oscillatory motion of a respective oscillation frequency () within an ion analyser apparatus. The method comprises acquiring a data set comprising a first measured signal frequency (.sub.1) associated with a first part of a measured image-charge/current signal of an ion and a second measured signal frequency (.sub.2) associated with a subsequent second part of the measured image-charge/current signal of the ion. The method includes estimating a charge state (Q) of the ion undergoing oscillatory motion of said first measured signal frequency (.sub.1) and subsequently of said second measured signal frequency (.sub.2) and therewith estimating the value of a mass change m to substantially match a reference mass corresponding to a mass of one or more neutral loss. The method includes estimating the mass (M) of a deprotonated molecule forming a part of the ion according to the estimated charge state (Q) of the ion, the first measured signal frequency (.sub.1), the quantified mass change value m, and the mass-to-charge ratio (m.sub.p/e) of a protonating proton.

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.

Systems and methods are used to analyze a sample using variable detection scan resolutions. A tandem mass spectrometer is instructed to perform at least two scans of a sample with different detection scan resolutions using a processor. The tandem mass spectrometer includes a mass analyzer that allows variable detection scan resolutions. The selection of the different detection scan resolutions can be based on one or more properties of sample compounds. The properties may include a sample compound molecular weight distribution that is calculated from a molecular weight distribution of expected compounds or is determined from a list of molecular weights for one or more known compounds. The tandem mass spectrometer can also be instructed to perform an analysis of the sample before instructing the tandem mass spectrometer to perform the at least two scans of the sample.

A thermal analysis step, a molecule ionization step and a molecular structure analysis step are executed in parallel to a temperature increasing step. In the molecule ionization step, component molecules contained in gas evolved from a sample S due to temperature increase are ionized, and in the molecular structure analysis step, any selected ion out of molecular ions obtained in the molecule ionization step is dissociated to generate fragment ions corresponding to the structural factors of the molecule, and the structure of the molecule is analyzed on the basis of the fragment ions.

A method and apparatus for tandem mass spectrometry is disclosed. Precursor ions are fragmented and the fragments are accumulated in parallel, by converting an incoming stream of ions from an ion source (10) into a time separated sequence of multiple precursor ions which are then assigned to their own particular channel of a multi compartment collision cell (40). In this manner, precursor ion species, being allocated to their own dedicated fragmentation cell chambers (41, 42 . . . 43) within the fragmentation cell (40), can then be captured and fragmented by that dedicated fragmentation chamber at optimum energy and/or fragmentation conditions.

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.

This invention is related to a tandem mass spectrometric analysis method in ion trap mass analyzer. Such method comprise three stages as represented by selective isolation, collision induced disassociation and mass scanning of ion. At the collision induced isolation stage, this invention is expected to endow parent ion of certain mass-charge ratio with energy through resonance excitation by changing cycle of radio frequency signals, namely frequency of radio frequency voltage imposed on the ion trap; such high-energy ions produced through resonance excitation are to be disassociated through collision with neutral molecules in the ion trap, which will further generate product ion to realize tandem mass spectrometric analysis. Advantage of this method lies in the fact that it can realize collision induced disassociation by changing scanning cycle at the stage of collision induced disassociation stage through software configuration, which can significantly simplify experimental devices and methods for tandem mass spectrometric analysis.

The present invention relates to newborn screening kits, methods, stable isotopically-labeled internal standards or internal standard solution for high throughput screening and analysis of metabolic disorders using liquid chromatography mass spectrometry (LC-MS) are provided. The metabolic disorders can be amino acid, organic acid or fatty acid oxidation disorders, and particularly urea cycle disorders or deficiencies, hyperammonemia, Hyperornithinemia-hyperammonemia-homocitrullinuria (HHH), and/or argininosuccinic aciduria. The newborn screening kits, methods, stable isotopically-labeled internal standards or internal standard solution are particularly useful for newborn screening (NBS) of metabolic disorders.