Abstract: A method for detecting a list of known biopolymer molecules comprises: calculating, for each biopolymer, a respective list of oligomer molecules predicted to be produced by chemical processing; calculating, for each oligomer molecule, a respective predicted chromatographic elution time period; assigning, for each biopolymer molecule, one or more selected oligomer molecules to be detected, wherein the selecting is performed using weighted selection probabilities determined from the predicted elution times; scheduling a plurality of oligomer detection events of a detection system, wherein each oligomer detection event corresponds to a respective one of the predicted elution time periods; performing the chemical reaction or processing of the sample to generate a processed sample; introducing the processed sample into a chromatographic system; introducing any eluting oligomers into the detection system; and operating the detection system so as to search for each of the selected oligomer molecules in accordance wi

Abstract: Disclosed herein are isobaric labeling reagent sets useful for multiplexed quantitation of peptides. The isobaric labeling reagent sets include a collection of at least two isobaric labeling reagents having first and second reporter groups with the same nominal mass but different isotopic substitutions and consequently different exact masses. Mass spectrometric analysis of the labeled samples is performed using a mass analyzer, such as an Orbitrap mass analyzer, capable of adequately resolving the ions of the first and second reporter groups. Reagent sets of the foregoing description may provide a degree of multiplexing in reporter ion quantitation experiments that is expanded relative to conventional labeling reagent sets, thereby reducing the number of chromatographic runs required for analysis and improving sample throughput.

Abstract: A novel scanning method of a mass spectrometer apparatus is introduced so as to relate by simple time shifts, rather than time dilations, the component signal (“peak”) from each ion even to an arbitrary reference signal produced by a desired homogeneous population of ions. Such a method and system, as introduced herein, is enabled in a novel fashion by scanning exponentially the RF and DC voltages on a quadrupole mass filter versus time while maintaining the RF and DC in constant proportion to each other. In such a novel mode of operation, ion intensity as a function of time is the convolution of a fixed peak shape response with the underlying (unknown) distribution of discrete mass-to-charge ratios (mass spectrum). As a result, the mass distribution can be reconstructed by deconvolution, producing a mass spectrum with enhanced sensitivity and mass resolving power.

Abstract: Disclosed herein are isobaric labeling reagent sets useful for multiplexed quantitation of peptides. The isobaric labeling reagent sets include a collection of at least two isobaric labeling reagents having first and second reporter groups with the same nominal mass but different isotopic substitutions and consequently different exact masses. Mass spectrometric analysis of the labeled samples is performed using a mass analyzer, such as an Orbitrap mass analyzer, capable of adequately resolving the ions of the first and second reporter groups. Reagent sets of the foregoing description may provide a degree of multiplexing in reporter ion quantitation experiments that is expanded relative to conventional labeling reagent sets, thereby reducing the number of chromatographic runs required for analysis and improving sample throughput.

Abstract: A method for detecting a list of known biopolymer molecules comprises: calculating, for each biopolymer, a respective list of oligomer molecules predicted to be produced by chemical processing; calculating, for each oligomer molecule, a respective predicted chromatographic elution time period; assigning, for each biopolymer molecule, one or more selected oligomer molecules to be detected, wherein the selecting is performed using weighted selection probabilities determined from the predicted elution times; scheduling a plurality of oligomer detection events of a detection system, wherein each oligomer detection event corresponds to a respective one of the predicted elution time periods; performing the chemical reaction or processing of the sample to generate a processed sample; introducing the processed sample into a chromatographic system; introducing any eluting oligomers into the detection system; and operating the detection system so as to search for each of the selected oligomer molecules in accordance wi

Abstract: A novel scanning method of a mass spectrometer apparatus is introduced so as to relate by simple time shifts, rather than time dilations, the component signal (“peak”) from each ion even to an arbitrary reference signal produced by a desired homogeneous population of ions. Such a method and system, as introduced herein, is enabled in a novel fashion by scanning exponentially the RF and DC voltages on a quadrupole mass filter versus time while maintaining the RF and DC in constant proportion to each other. In such a novel mode of operation, ion intensity as a function of time is the convolution of a fixed peak shape response with the underlying (unknown) distribution of discrete mass-to-charge ratios (mass spectrum). As a result, the mass distribution can be reconstructed by deconvolution, producing a mass spectrum with enhanced sensitivity and mass resolving power.

Abstract: Disclosed herein are isobaric labeling reagent sets useful for multiplexed quantitation of peptides. The isobaric labeling reagent sets include a collection of at least two isobaric labeling reagents having first and second reporter groups with the same nominal mass but different isotopic substitutions and consequently different exact masses. Mass spectrometric analysis of the labeled samples is performed using a mass analyzer, such as an Orbitrap mass analyzer, capable of adequately resolving the ions of the first and second reporter groups. Reagent sets of the foregoing description may provide a degree of multiplexing in reporter ion quantitation experiments that is expanded relative to conventional labeling reagent sets, thereby reducing the number of chromatographic runs required for analysis and improving sample throughput.

Abstract: Disclosed herein are isobaric labeling reagent sets useful for multiplexed quantitation of peptides. The isobaric labeling reagent sets include a collection of at least two isobaric labeling reagents having first and second reporter groups with the same nominal mass but different isotopic substitutions and consequently different exact masses. Mass spectrometric analysis of the labeled samples is performed using a mass analyzer, such as an Orbitrap mass analyzer, capable of adequately resolving the ions of the first and second reporter groups. Reagent sets of the foregoing description may provide a degree of multiplexing in reporter ion quantitation experiments that is expanded relative to conventional labeling reagent sets, thereby reducing the number of chromatographic runs required for analysis and improving sample throughput.

Abstract: A novel scanning method of a mass spectrometer apparatus is introduced so as to relate by simple time shifts, rather than time dilations, the component signal (“peak”) from each ion even to an arbitrary reference signal produced by a desired homogeneous population of ions. Such a method and system, as introduced herein, is enabled in a novel fashion by scanning exponentially the RF and DC voltages on a quadrupole mass filter versus time while maintaining the RF and DC in constant proportion to each other. In such a novel mode of operation, ion intensity as a function of time is the convolution of a fixed peak shape response with the underlying (unknown) distribution of discrete mass-to-charge ratios (mass spectrum). As a result, the mass distribution can be reconstructed by deconvolution, producing a mass spectrum with enhanced sensitivity and mass resolving power.

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: A novel scanning method of a mass spectrometer apparatus is introduced so as to relate by simple time shifts, rather than time dilations, the component signal (“peak”) from each ion even to an arbitrary reference signal produced by a desired homogeneous population of ions. Such a method and system, as introduced herein, is enabled in a novel fashion by scanning exponentially the RF and DC voltages on a quadrupole mass filter versus time while maintaining the RF and DC in constant proportion to each other. In such a novel mode of operation, ion intensity as a function of time is the convolution of a fixed peak shape response with the underlying (unknown) distribution of discrete mass-to-charge ratios (mass spectrum). As a result, the mass distribution can be reconstructed by deconvolution, producing a mass spectrum with enhanced sensitivity and mass resolving power.

Abstract: A method of acquiring and compiling data obtained on a mass spectrometer system, comprises: (a) generating a multiplexed mass spectrum comprising a superposed plurality of product-ion mass spectra comprising a plurality of product-ion types, each product-ion mass spectrum corresponding to fragmentation of a respective precursor-ion type, each precursor-ion type and each product ion type having a respective mass-to-charge (m/z) ratio; (b) decomposing the multiplexed product-ion mass spectrum so as to recognize relative abundances of previously-observed product-ion mass spectra within the multiplexed product-ion mass spectrum, the decomposing employing a mass-spectral library having a plurality of entries corresponding to respective product ion mass spectra previously-observed on said mass spectrometer system; (c) recognizing an additional contribution to the multiplexed mass spectrum that is neither attributable to random variation nor to any previously-observed product-ion spectrum; and (d) storing at least o

Abstract: A method of acquiring and interpreting data using (i) a mass spectrometer system operated according to a set of operating conditions and (ii) a mass spectral library having a plurality of library entries derived from data previously obtained using said mass spectrometer system operated according to said set of operating conditions comprising: (a) generating, using the mass spectrometer system, a multiplexed mass spectrum comprising a superposition of a plurality of product-ion mass spectra comprising a plurality of product-ion types, each product-ion mass spectrum corresponding to fragmentation of a respective precursor-ion type formed by ionization of the plurality of chemical compounds, each precursor-ion type having a respective precursor-ion mass-to-charge (m/z) ratio and each product ion type having a respective product-ion m/z ratio; and (b) decomposing the multiplexed product-ion mass spectrum, using the mass-spectral library, so as to calculate relative abundances of previously-observed product-ion ma

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: Disclosed herein are isobaric labeling reagent sets useful for multiplexed quantitation of peptides. The isobaric labeling reagent sets include a collection of at least two isobaric labeling reagents having first and second reporter groups with the same nominal mass but different isotopic substitutions and consequently different exact masses. Mass spectrometric analysis of the labeled samples is performed using a mass analyzer, such as an Orbitrap mass analyzer, capable of adequately resolving the ions of the first and second reporter groups. Reagent sets of the foregoing description may provide a degree of multiplexing in reporter ion quantitation experiments that is expanded relative to conventional labeling reagent sets, thereby reducing the number of chromatographic runs required for analysis and improving sample throughput.

Abstract: Methods of tandem mass spectrometry are disclosed, characterized by: providing a mixture of precursor ions comprising a plurality of individually isolated ion types of respective selected m/z ratios; estimating an elemental composition for each precursor ion type based on its respective m/z ratio; generating a sample of fragment ions comprising a plurality of fragment ion types by fragmenting the plurality of precursor ion types of the mixture; generating a mass spectrum of the fragment ion types to determine a respective m/z ratio or m/z ratio range for each respective fragment ion type; estimating an elemental composition for each fragment ion type based on its respective m/z ratio or m/z ratio range; and calculating probabilities, for each precursor ion type, that a fragment ion type or a pair of fragment ion types was derived from said precursor ion type.

Abstract: Methods of tandem mass spectrometry are disclosed, characterized by: providing a mixture of precursor ions comprising a plurality of individually isolated ion types of respective selected m/z ratios; estimating an elemental composition for each precursor ion type based on its respective m/z ratio; generating a sample of fragment ions comprising a plurality of fragment ion types by fragmenting the plurality of precursor ion types of the mixture; generating a mass spectrum of the fragment ion types to determine a respective m/z ratio or m/z ratio range for each respective fragment ion type; estimating an elemental composition for each fragment ion type based on its respective m/z ratio or m/z ratio range; and calculating probabilities, for each precursor ion type, that a fragment ion type or a pair of fragment ion types was derived from said precursor ion type.

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: 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