Thermo Finnigan LLC

Justin Blethrow

Michael W Senko

Robert Alois Grothe, Jr

Philip M Remes

Vladimir Zabrouskov

Shannon Eliuk Dixon

Eric Hemenway

Tonya Second

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.

Hybrid mass spectrometer and methods of operating a mass spectrometer

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.

Method for highly multiplexed quantitation of peptides by mass spectrometry and labeling reagent sets therefor

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.

Methods for predictive automatic gain control for hybrid mass spectrometers

Method for highly multiplexed quantitation of peptides by mass spectrometry and mass labels therefor

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Oakland, CA, United States of America

Justin Blethrow