Abstract: A novel method and mass spectrometer apparatus is introduced to spatially and temporally resolve images of one or more ion exit patterns of a multipole instrument. In particular, the methods and structures of the present invention measures the ion current as a function of time and spatial displacement in the beam cross-section of a quadrupole mass filter via an arrayed detector. The linearity of the detected quadrupole ion current in combination with it reproducible spatial-temporal structure enables the deconvolution of the contributions of signals from individual ion species in complex mixtures where both sensitivity and mass resolving power are essential.

Abstract: The present invention comprises a method and system for accurate estimation of the ion cyclotron resonance (ICR) parameters in Fourier-transform mass spectrometry (FTMS/FT-ICR MS). The parameters are essential to estimating the mass to charge ratio of an ion from FT-ICR MS data, the intended purpose of the instrument. Achieving greater accuracy in the parameters assists in greater accuracy of the mass to charge ratio of an ion, and obtaining an accurate estimation of the mass to charge ratio of an ion further aides in detecting mass with sub-ppm accuracy. Estimating mass in this manner enhances identification and characterization of large molecules. The inventive method and system thereby enhances the data obtained by conventional FTMS by accurately estimating ICR parameters. Ultimately, accurate estimates of the masses of molecules and detection and characterization of molecules from FT-ICR MS data are obtained.

Abstract: Described herein are methods that may be used related to mass spectrometry, such as mass spectrometry analysis, mass spectrometry calibration, identification of proteins/peptides by mass spectrometry and/or mass spectrometry data collection strategies. In one embodiment, the subject matter discloses a phase-modeling analysis method for identification of proteins or peptides by mass spectrometry.

Abstract: Described herein are methods that may be used related to mass spectrometry, such as mass spectrometry analysis, mass spectrometry calibration, identification of proteins/peptides by mass spectrometry and/or mass spectrometry data collection strategies. In one embodiment, the subject matter discloses a phase-modeling analysis method for identification of proteins or peptides by mass spectrometry.

Abstract: Described herein are methods that may be used related to mass spectrometry, such as mass spectrometry analysis, mass spectrometry calibration, identification of proteins/peptides by mass spectrometry and/or mass spectrometry data collection strategies. In one embodiment, the subject matter discloses a phase-modeling analysis method for identification of proteins or peptides by mass spectrometry.

Abstract: There is provided a method of automatically identifying and characterizing spectral peaks of a spectrum generated by an analytical apparatus and reporting information relating to the spectral peaks to a user, comprising the steps of receiving the spectrum generated by the analytical apparatus; automatically subtracting a baseline from the spectrum so as to generate a baseline-corrected spectrum; automatically detecting and characterizing the spectral peaks in the baseline-corrected spectrum; and reporting at least one item of information relating to each detected and characterized spectral peak to a user. In embodiments, baseline model curve parameters or peak model curve parameters are neither input by nor exposed to the user prior to the reporting step.

Abstract: The present invention comprises a method and system for accurate estimation of the ion cyclotron resonance (ICR) parameters in Fourier-transform mass spectrometry (FTMS/FT-ICR MS). The parameters are essential to estimating the mass to charge ratio of an ion from FT-ICR MS data, the intended purpose of the instrument. Achieving greater accuracy in the parameters assists in greater accuracy of the mass to charge ratio of an ion, and obtaining an accurate estimation of the mass to charge ratio of an ion further aides in detecting mass with sub-ppm accuracy. Estimating mass in this manner enhances identification and characterization of large molecules. The inventive method and system thereby enhances the data obtained by conventional FTMS by accurately estimating ICR parameters. Ultimately, accurate estimates of the masses of molecules and detection and characterization of molecules from FT-ICR MS data are obtained.

Abstract: The invention relates to a mass spectrometry calibration system that may be performed in real-time using the information contained within a sample without the addition of specific calibrants. When applied to a sample, such as a proteomic sample, the calibration system may identify the exact masses of peptides in the sample. The system involves the use of mathematical algorithms that iteratively estimate the error in the measurement and update the calibration parameters accordingly; thereby resulting in peptide mass identification.

Abstract: The invention relates to a mass spectrometry calibration system that may be performed in real-time using the information contained within a sample without the addition of specific calibrants. When applied to a sample, such as a proteomic sample, the calibration system may identify the exact masses of peptides in the sample. The system involves the use of mathematical algorithms that iteratively estimate the error in the measurement and update the calibration parameters accordingly; thereby resulting in peptide mass identification.

Abstract: Methods of tandem mass spectrometry (MS/MS) for use in a mass spectrometer are disclosed, the methods characterized by the steps of: (a) providing a sample of precursor ions comprising a plurality of ion types, each ion type comprising a respective range of masses; (b) generating a mass spectrum of the precursor ions using the mass spectrometer so as to determine a respective mass value or mass value range for each of the precursor ion types; (c) estimating an elemental composition for each of the precursor ion types based on the mass value or mass value range determined for each respective ion type; (d) generating a sample of fragment ions comprising plurality of fragment ion types by fragmenting the plurality of precursor ion types within the mass spectrometer; (d) generating a mass spectrum of the fragment ion types so as to determine a respective mass value or mass value range for each respective fragment ion type; (e) estimating an elemental composition for each of the fragment ion types based on the mas

Abstract: There is provided a method of automatically identifying and characterizing spectral peaks of a spectrum generated by an analytical apparatus and reporting information relating to the spectral peaks to a user, comprising the steps of receiving the spectrum generated by the analytical apparatus; automatically subtracting a baseline from the spectrum so as to generate a baseline-corrected spectrum; automatically detecting and characterizing the spectral peaks in the baseline-corrected spectrum; and reporting at least one item of information relating to each detected and characterized spectral peak to a user. In embodiments, baseline model curve parameters or peak model curve parameters are neither input by nor exposed to the user prior to the reporting step.

Abstract: A novel method and mass spectrometer apparatus is introduced to spatially and temporally resolve images of one or more ion exit patterns of a multipole instrument. In particular, the methods and structures of the present invention measures the ion current as a function of time and spatial displacement in the beam cross-section of a quadrupole mass filter via an arrayed detector. The linearity of the detected quadrupole ion current in combination with it reproducible spatial-temporal structure enables the deconvolution of the contributions of signals from individual ion species in complex mixtures where both sensitivity and mass resolving power are essential.

Abstract: There is provided a method of automatically identifying and characterizing spectral peaks of a spectrum generated by an analytical apparatus and reporting information relating to the spectral peaks to a user, comprising the steps of: receiving the spectrum generated by the analytical apparatus; automatically subtracting a baseline from the spectrum so as to generate a baseline-corrected spectrum; automatically detecting and characterizing the spectral peaks in the baseline-corrected spectrum; and reporting at least one item of information relating to each detected and characterized spectral peak to a user. In embodiments, baseline model curve parameters or peak model curve parameters are neither input by nor exposed to the user prior to the reporting step.

Abstract: There is provided a method of automatically identifying and characterizing spectral peaks of a spectrum generated by an analytical apparatus and reporting information relating to the spectral peaks to a user, comprising the steps of: receiving the spectrum generated by the analytical apparatus; automatically subtracting a baseline from the spectrum so as to generate a baseline-corrected spectrum; automatically detecting and characterizing the spectral peaks in the baseline-corrected spectrum; and reporting at least one item of information relating to each detected and characterized spectral peak to a user. In embodiments, baseline model curve parameters or peak model curve parameters are neither input by nor exposed to the user prior to the reporting step.

Abstract: The present invention comprises a method and system for accurate estimation of the ion cyclotron resonance (ICR) parameters in Fourier-transform mass spectrometry (FTMS/FT-ICR MS). The parameters are essential to estimating the mass to charge ratio of an ion from FT-ICR MS data, the intended purpose of the instrument. Achieving greater accuracy in the parameters assists in greater accuracy of the mass to charge ratio of an ion, and obtaining an accurate estimation of the mass to charge ratio of an ion further aides in detecting mass with sub-ppm accuracy. Estimating mass in this manner enhances identification and characterization of large molecules. The inventive method and system thereby enhances the data obtained by conventional FTMS by accurately estimating ICR parameters. Ultimately, accurate estimates of the masses of molecules and detection and characterization of molecules from FT-ICR MS data are obtained.

Abstract: The invention relates to a mass spectrometry calibration system that may be performed in real-time using the information contained within a sample without the addition of specific calibrants. When applied to a sample, such as a proteomic sample, the calibration system may identify the exact masses of peptides in the sample. The system involves the use of mathematical algorithms that iteratively estimate the error in the measurement and update the calibration parameters accordingly; thereby resulting in peptide mass identification.