Abstract: A hybrid mass spectrometer design and architecture, and methods of operating mass spectrometers are disclosed. According to one operating method, an analysis time is determined for each one of a plurality of ion species to be analyzed in an ordered sequence, and an injection time is calculated for at least some of the ion species based on an analysis time of a preceding ion species in the ordered list. The method enables more efficient utilization of analyzer time.

Abstract: A hybrid mass spectrometer design and architecture, and methods of operating mass spectrometers are disclosed. According to one operating method, an analysis time is determined for each one of a plurality of ion species to be analyzed in an ordered sequence, and an injection time is calculated for at least some of the ion species based on an analysis time of a preceding ion species in the ordered list. The method enables more efficient utilization of analyzer time.

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 mass analyzing ions comprising a restricted range mass-to-charge (m/z) ratios comprising (i) performing a survey mass analysis, using a first mass analyzer employing indirect detection of ions by image current detection, to measure a flux of ions having m/z ratios within said range and (ii) performing a dependent mass analysis, using a second mass analyzer, of an optimal quantity of ions having m/z ratios within said range, said optimal quantity collected for a time period determined by the measured ion flux, the method characterized in that: the time period is determined using a corrected ion flux that includes a correction that comprises an estimate of the quantity of ions that are undetected by the first mass analyzer.

Abstract: A hybrid mass spectrometer design and architecture, and methods of operating mass spectrometers are disclosed. According to one operating method, an analysis time is determined for each one of a plurality of ion species to be analyzed in an ordered sequence, and an injection time is calculated for at least some of the ion species based on an analysis time of a preceding ion species in the ordered list. The method enables more efficient utilization of analyzer time.

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 mass analyzing ions comprising a restricted range mass-to-charge (m/z) ratios comprising (i) performing a survey mass analysis, using a first mass analyzer employing indirect detection of ions by image current detection, to measure a flux of ions having m/z ratios within said range and (ii) performing a dependent mass analysis, using a second mass analyzer, of an optimal quantity of ions having m/z ratios within said range, said optimal quantity collected for a time period determined by the measured ion flux, the method characterized in that: the time period is determined using a corrected ion flux that includes a correction that comprises an estimate of the quantity of ions that are undetected by the first mass analyzer.

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 method for mass analyzing ions comprising a restricted range mass-to-charge (m/z) ratios comprising (i) performing a survey mass analysis, using a first mass analyzer employing indirect detection of ions by image current detection, to measure a flux of ions having m/z ratios within said range and (ii) performing a dependent mass analysis, using a second mass analyzer, of an optimal quantity of ions having m/z ratios within said range, said optimal quantity collected for a time period determined by the measured ion flux, the method characterized in that: the time period is determined using a corrected ion flux that includes a correction that comprises an estimate of the quantity of ions that are undetected by the first mass analyzer.

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: 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.