Methods are described for measuring the amount of a vitamin B2 in a sample. More specifically, mass spectrometric methods are described for detecting and quantifying vitamin B2 in a sample utilizing on-line extraction methods coupled with tandem mass spectrometric techniques.

Apparatus is provided and an IDA method is modified to detect and separately dissociate alkali-metal adducts of a compound. An ion source device ionizes one or more compounds of a sample, producing an ion beam. A mass filter selects a mass range of precursor ions from the ion beam, a mass analyzer measures intensities and m/z values of the precursor ions, and one or more of the precursor ions are selected for a peak list. For each pair of precursor ions of the peak list, if an m/z difference between the pair corresponds to an m/z difference between an alkali metal ion and another alkali metal ion or a proton, an ExD device is used to dissociate one precursor ion or both precursor ions of the pair using the processor. A CID device is used to dissociate all other precursor ions of the peak list.

A method of mass spectrometry determines if a mutated variant of a target protein is present in a sample. The method includes subjecting the sample to fragmentation so as to cause the target protein to fragment to form second generation fragment ions, and then mass analysing these fragment ions to obtain spectral data. The method determines if a mutated variant is present in the sample by determining that an ion in the spectral data has a mass to charge ratio that differs from the mass to charge ratio of an ion that would be observed if the target protein was a normal unmutated version of the target protein, and by an amount that corresponds to a mass difference that would be caused by the target protein being a mutated variant of the target protein.

Methods are described for measuring the amount of a vitamin B2 in a sample. More specifically, mass spectrometric methods are described for detecting and quantifying vitamin B2 in a sample utilizing on-line extraction methods coupled with tandem mass spectrometric techniques.

Methods are described for measuring the amount of a vitamin B2 in a sample. More specifically, mass spectrometric methods are described for detecting and quantifying vitamin B2 in a sample utilizing on-line extraction methods coupled with tandem mass spectrometric techniques.

A mass isolation device selects a precursor ion of a sample that has been digested using a protease. A first fragmentation device fragments the precursor ion using collision-induced dissociation (CID), and the resulting product ions are analyzed using a mass analyzer producing a CID spectrum. A list of theoretical candidate glycopeptide sequences is determined from CID spectrum. The mass isolation device again selects the precursor ion of the sample. A second fragmentation device fragments the precursor ion using electron-based dissociation (ExD), and the resulting product ions are analyzed using the mass analyzer producing a CID spectrum. For each sequence of the list, the sequence is computationally fragmented, producing theoretical fragments, mass-to-charge ratio (m/z) values are calculated for the theoretical fragments, and the sequence is scored using c and z fragment matching rules. The highest scoring sequence is identified as a peptide sequence of a glycopeptide of the sample.

A calibration apparatus for a mass analyzer includes an ion source device and a dual-purpose electron beam generating unit. The ion source device ionizes an analyte of a sample, producing analyte ions. The dual-purpose electron beam generating unit is positioned between the ion source device and the mass analyzer. In a first mode, the dual-purpose electron beam generating unit is used to create fragments of analyte ions of unknown mass-to-charge ratio. In a second mode, the dual-purpose electron beam generating unit is used to create ions of calibration compounds of known mass-to-charge ratio. All ions are subsequently transferred to the mass analyzer.

Methods are described for using a combination of mass spectroscopic and proteomic approaches for identifying the specific pairing of heavy and light chains for an intact antibody, an antibody fragment, a mixture of intact antibodies, or a mixture of antibody fragments.

A mass spectrometer is operated to simultaneously measure precursor and production data over a number of acquisitions. For each acquisition, the following steps are performed. Ion transfer optics inject ions from an ion beam into an ELIT causing the ions to oscillate axially between two electric fields produced by two the sets of reflectrons. The ELIT measures a time domain image current of the oscillating ions from ion injection to a total acquisition time, Tacq1, and fragments the oscillating ions at one or both turning points of the oscillating ions adding product ions to the oscillating ions. The fragmentation is performed at a delay time relative to the ion injection that is increased by a time increment in each subsequent acquisition making the fragmentation dependent on ion position. The measured time domain image current is stored as a row or column of a two-dimensional matrix.

A linear ion trap system includes a linear ion trap having at least two discrete trapping regions for processing ions. An RF electrical potential generator produces two RF waveforms applied to a pair of pole electrodes of the linear ion trap forming a RF trapping field component to trap ions radially. A multi-output DC electrical potential generator produces a first set of multiple DC field components superimposed to the RF trapping field component and distributed across the length of the linear ion trap to control ions axially. A control unit is configured to switch the DC electrical potentials and DC field components collectively forming a first trapping region of the at least two discrete trapping regions that is populated with ions to alter ion potential energy from a first level to a second level, and to enable at least a first ion processing step in at least one of the first and second levels.