Abstract: This system and method disclosed herein are configured to improve high mass range ion trap performance by use of a multi-directional segmented scan approach. In some embodiments of the system and method disclosed herein, the mass range of conventional ion trap technology may be extended/increased without changing the hardware or compromising lower range mass/charge efficiency. Specifically, the system and methods disclosed herein use a segmented, bi-directional scan that increases the mass range of an ion trap mass spectrometer and circumvents the problem of mass discrimination during mass analysis in the high Thompson value range.

Abstract: This invention relates to tandem mass spectrometry and, in particular, to tandem mass spectrometry using a linear ion trap and a time of flight detector to collect mass spectra to form a MS/MS experiment. The accepted standard is to store and mass analyze precursor ions in the ion trap before ejecting the ions axially to a collision cell for fragmentation before mass analysis of the fragments in the time of flight detector. This invention makes use of orthogonal ejection of ions with a narrow range of m/z values to produce a ribbon beam of ions that are injected into the collision cell. The shape of this beam and the high energy of the ions are accommodated by using a planar design of collision cell. Ions are retained in the ion trap during ejection so that successive narrow ranges may be stepped through consecutively to cover all precursor ions of interest.

Abstract: Methods and apparatus for data-dependent mass spectrometric MS/MS or MSn analysis are disclosed. The methods may include determination of the charge state of an ion species of interest, followed by automated selection of a dissociation type (e.g., CAD, ETD, or ETD followed by a non-dissociative charge reduction or collisional activation) based at least partially on the determined charge state. The ion species of interest is then dissociated in accordance with the selected dissociation type, and an MS/MS or MSn spectrum of the resultant product ions may be acquired.

Abstract: The present invention relates to a new method for identifying polypeptides by deducing the amino acid sequence of the carboxy and amino termini by a mass spectrometer analysis. The method comprises the steps of dissociating highly charged peptide precursor ions (e.g., z>4) using electron transfer dissociation inducing anions followed by removal of those reagents and introduction of a second, proton transfer inducing anion type. The second PTR reaction duration is adjusted to convert the ETD products to primarily the +1 charge-state to reduce the highly charged c and z-type fragments, producing an m/z spectrum containing a series of c and z-type fragment ions that are easily interpreted to reveal the sequence of the amino and carboxy terminus, respectively.

Abstract: Ions in a predefined narrow mass to charge ratio range are isolated in an ion trap by adjusting the field and using ejection frequency waveform(s). The ejection waveforms have frequency components in a first and a second dimension, and, are applied across electrodes aligned along a first and a second dimension. Thus the mass-to-charge ratio isolation window is controlled and has an improved resolution without increasing the number of frequency components.

Abstract: This invention relates to tandem mass spectrometry and, in particular, to tandem mass spectrometry using a linear ion trap and a time of flight detector to collect mass spectra to form a MS/MS experiment. The accepted standard is to store and mass analyze precursor ions in the ion trap before ejecting the ions axially to a collision cell for fragmentation before mass analysis of the fragments in the time of flight detector. This invention makes use of orthogonal ejection of ions with a narrow range of m/z values to produce a ribbon beam of ions that are injected into the collision cell. The shape of this beam and the high energy of the ions are accommodated by using a planar design of collision cell. Ions are retained in the ion trap during ejection so that successive narrow ranges may be stepped through consecutively to cover all precursor ions of interest.

Abstract: Methods and apparatus for trapping or guiding ions. Ions are introduced into an ion trap or ion guide. The ion trap or ion guide includes a first set of electrodes and a second set of electrodes. The first set of electrodes defines a first portion of an ion channel to trap or guide the introduced ions. Periodic voltages are applied to electrodes in the first set of electrodes to generate a first oscillating electric potential that radially confines the ions in the ion channel, and periodic voltages are applied to electrodes in the second set of electrodes to generate a second oscillating electric potential that axially confines the ions in the ion channel.

Abstract: Ions in a predefined narrow mass to charge ratio range are isolated in an ion trap by adjusting the field and using ejection frequency waveform(s). Thus the mass-to-charge ratio isolation window is controlled and has an improved resolution without increasing the number of frequency components.

Abstract: Methods and apparatus for trapping or guiding ions. Ions are introduced into an ion trap or ion guide. The ion trap or ion guide includes a first set of electrodes and a second set of electrodes. The first set of electrodes defines a first portion of an ion channel to trap or guide the introduced ions. Periodic voltages are applied to electrodes in the first set of electrodes to generate a first oscillating electric potential that radially confines the ions in the ion channel, and periodic voltages are applied to electrodes in the second set of electrodes to generate a second oscillating electric potential that axially confines the ions in the ion channel.

Abstract: The present invention relates to a new method for fragmenting ions in a mass spectrometer through the use of electron transfer dissociation, and for performing sequence analysis of peptides and proteins by mass spectrometry. In the case of peptides, the invention promotes fragmentation along the peptide backbone and makes it possible to deduce the amino acid sequence of the sample, including modified amino acid residues, through the use of an RF field device.