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Thermo Finnigan Llc patents


Recent patent applications related to Thermo Finnigan Llc. Thermo Finnigan Llc is listed as an Agent/Assignee. Note: Thermo Finnigan Llc may have other listings under different names/spellings. We're not affiliated with Thermo Finnigan Llc, we're just tracking patents.

ARCHIVE: New 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 | Company Directory "T" | Thermo Finnigan Llc-related inventors


Systems and methods for scaling injection waveform amplitude during ion isolation

This disclosure describes a method of adjusting the amplitude of broadband waveforms for isolation, especially during injection to a multipole trapping device. Isolation during injection to a trapping device is known to be an effective way of accumulating a desired population of ions while rejecting unwanted species. ... Thermo Finnigan Llc

Methods for mass spectrometry of mixtures of protein or polypeptides using proton transfer reaction

A method comprises: (1) making an extract of a biological sample; (2) repeatedly: (a) choosing a respective one of a plurality of pre-determined protein or polypeptide analyte compounds; (b) introducing a portion of the extract into an electrospray ionization source, thereby generating positive ions comprising a plurality of ion species; (c) isolating a plurality of subsets of the ion species comprising respective mass-to-charge (m/z) ratio ranges, each range including an m/z ratio corresponding to a respective protonation state of the chosen compound; (d) reacting the isolated plurality of subsets of first-generation ion species with proton transfer reaction reagent anions for a pre-determined time duration; (e) generating a mass spectrum of the product ion species; and (g) identifying either the presence or absence of the compound based on the mass spectrum; and (3) identifying the presence or absence of the microorganism within the sample based on analytes present.. . ... Thermo Finnigan Llc

Methods and apparatus for tandem collision-induced dissociation cells

A mass spectrometer system comprises: (a) an ion source; (b) a mass filter; (c) a mass analyzer; (d) a partitioned ion fragmentation cell configured to receive ions from the mass filter and to outlet fragment ions to the mass analyzer comprising: (d1) a set of multipole rod electrodes; a housing enclosing the set of multipole rod electrodes and comprising an ion inlet and an ion outlet; (d2) a set of partitions within the housing separating the housing interior into a plurality of compartments; and (d3) a plurality of gas inlets, each gas inlet fluidically coupled to a source of a collision gas and to a respective compartment and having a respective inlet shutoff valve; and (e) a controller electrically coupled to each inlet shutoff valve and configured to independently control the pressure of collision gas within each compartment.. . ... Thermo Finnigan Llc

System and method for real-time isotope identification

An embodiment of a method for real time material identification is described that comprises determining an approximate mass value for an unknown material from spectral information derived from mass spectral analysis of the unknown material; retrieving profile models that correspond to a known material from a data structure using the approximate mass value; fitting a sample profile for the unknown material from the spectral information to the profile models to generate a fit score for each fit, wherein the lowest fit score corresponds to the best fit; calculating a mass value from the best fitting profile model and the sample profile.. . ... Thermo Finnigan Llc

Ion interface device having multiple confinement cells and methods of use thereof

A device and associated method are disclosed for interfacing an ion trap to a pulsed mass analyzer (such as a time-of-flight analyzer) in a mass spectrometer. The device includes a plurality of separate confinement cells and structures for directing ions into a selected one of the confinement cells. ... Thermo Finnigan Llc

Methods for calibration of a quadrupole mass filter

The linear relationship between physical mass-to-charge ratio and the location of a mass spectral peak along the dc/rf scan line of a quadrupole mass filter is used to simultaneously identify a known set of calibrants and to determine the correct slope and scaling of the scan line from a full spectrum scan of an uncalibrated instrument. This is achieved by using a method for image feature detection, to find a set of collinear peaks in a two-dimensional image constructed from scaled versions of the mass spectrum. ... Thermo Finnigan Llc

Hybrid mass spectrometer and methods of operating a mass spectrometer

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. ... Thermo Finnigan Llc

Methods for operating electrostatic trap mass analyzers

A method of operating an electrostatic trapping mass analyzer, comprising: introducing a sample of ions into a trapping region of the mass analyzer, wherein a trapping field within the trapping region is such that the ions exhibit radial motion with respect to a central longitudinal axis of the trapping region while undergoing harmonic motion in a dimension defined by the central longitudinal axis, the frequency of harmonic motion of a particular ion being a function of its mass-to-charge ratio; superimposing a modulation field onto the trapping field within the trapping region, the modulation field acting to either increase or reduce the harmonic motion energies of the ions by an amount varying according to the frequency of harmonic motion; and acquiring a mass spectrum of the ions in the trapping region by measuring a signal representative of an image current induced by the harmonic motion of the ions.. . ... Thermo Finnigan Llc

Ion transfer tube flow and pumping system load

A mass spectrometer system can include an ion source, a vacuum chamber; a mass analyzer within the vacuum chamber, a transfer tube between the ion source and the vacuum chamber, a transfer tube heater, and a vacuum pump. The mass spectrometer system can be configured to reduce the pump speed of the vacuum pump in response to receiving a transfer tube swap instruction; lower the temperature of the transfer tube to below a first threshold; operating the vacuum pump at the reduced pump speed while the transfer tube is replaced with a second transfer tube; heating the second transfer tube to a temperature above a pump down temperature; and increasing the pump speed of the vacuum pump after the temperature of the second transfer tube exceeds a second threshold.. ... Thermo Finnigan Llc

Methods for transferring ions in a mass spectrometer

A method for transporting ions includes: providing an ion transfer tube having an axis and an internal bore having a width and a height less than the width; and providing an apparatus comprising a plurality of electrodes, each having a respective ion aperture having an aperture center, the apertures defining an ion channel configured to receive the ions from the ion transfer tube and to transport the ions to an outlet end of the apparatus, wherein at least a subset of the apertures progressively decrease in size in a direction towards the apparatus outlet end, wherein the ion transfer tube is configured such that the ion transfer tube axis is non-coincident with an axis of the ion channel or such that the width dimension of the ion transfer tube bore is parallel to a plane defined by the ion transfer tube axis and the ion channel axis.. . ... Thermo Finnigan Llc

Methods for optimizing mass spectrometer parameters

A method for determining optimal values of a mass spectral operating parameter for mass spectral analysis of each of a plurality of compounds comprises: acquiring a plurality of mass spectral measurements of each of at least one characteristic ion species of each respective compound during its introduction into a mass spectrometer while a quantity of each introduced compound varies with time wherein, for each characteristic ion species, the operational parameter is caused to vary between successive mass spectral measurements of the said species; calculating, for each characteristic ion species, a corrected intensity of at least a portion of the plurality of mass spectral measurements of said each species, based on a best-fit synthetic model curve that relates to the time variation of the respective corresponding compound; and determining the optimal values of the operating parameter from analyses of variation of the corrected intensities with respect to the operational parameter variation.. . ... Thermo Finnigan Llc

Methods of performing ion-ion reactions in mass spectrometry

A method is described that produces product ions for mass analysis, the method comprising the steps of: introducing precursor ions into an rf electric field ion containment device, introducing reagent ions into the rf electric field ion containment device and performing an ion-ion interaction in the rf electric field ion containment device by co-trapping the precursor ions with the reagent ions. Precursor ions and product ions may be retained and/or isolated in the rf electric field ion containment device. ... Thermo Finnigan Llc

Systems and methods for improving loading capacity of a segmented reaction cell by utilizing all available segments

A method for analyzing a sample includes trapping a first ion packet in a first segment of a multi-segment reaction cell; trapping a second ion packet in a second segment of the multi-segment reaction cell; and trapping a third ion packet in a third segment of the multi-segment reaction cell. At least one of the first, second, and third ion packets includes precursor ions, and at least another one of the first, second, and third ion packets includes reagent ions. ... Thermo Finnigan Llc

Mass spectrometry analysis of biomolecules by multiple charge state selection using a concurrent precursor isolation technique

A method is described for the analysis of biological polymers, for example, intact proteins or oligonucleotides, by mass spectrometry. This method produces sample ions from a sample containing biological polymers, and ion species are selected that correspond to different charge states of a biological polymer molecule. ... Thermo Finnigan Llc

11/30/17 / #20170345636

Systems and methods for reducing the kinetic energy spread of ions radially ejected from a linear ion trap

A system for analyzing a sample includes a linear ion trap, an insert dc electrode, a voltage controller, and an rf control circuitry. The linear ion trap includes a first pair of trap electrodes and a second pair of trap electrodes spaced apart from each other and surrounding a trap interior. ... Thermo Finnigan Llc

11/30/17 / #20170345632

Analyzing a complex sample by ms/ms using isotopically-labeled standards

A method and corresponding apparatus are disclosed for analysis of a peptide-containing sample. The sample is prepared by adding isotopically-labeled peptides corresponding to endogenous peptides of interest, and the prepared sample is analyzed by liquid chromatography-mass spectrometry (lcms). ... Thermo Finnigan Llc

11/30/17 / #20170345631

Systems and methods for grouping ms/ms transitions

A method for analyzing a sample includes identifying a plurality of precursors for analysis and grouping the precursors into two or more groups. The precursors are grouped such that for the precursors within a group the masses of ions of the precursors in the group are within a first mass range, and the number of precursors within the group is below a maximum allowable number of precursors. ... Thermo Finnigan Llc

11/23/17 / #20170338089

Systems and methods for sample comparison and classification

A system includes a database server and a plurality of processing nodes. The plurality of processing nodes are configured to receive mass spectrometry data from a plurality of samples; align the mass spectrometry data to correct for changes in retention time to generate a reference alignment; cluster compounds across the plurality of samples; store the reference alignment and clustered compound data to the database server; receive additional mass spectrometry data from additional samples; align the additional mass spectrometry data to a reference alignment within the database; correlate the compounds from the additional samples with the clustered compound data; classify the compounds; perform statistical analysis on the classified compounds to identify compounds meeting threshold criteria; and provide an indication of compounds meeting the threshold criteria.. ... Thermo Finnigan Llc

10/05/17 / #20170287687

Data independent acquisition with variable multiplexing degree

A method is disclosed for analyzing ions by mass spectrometry by repeatedly executing a data acquisition cycle to acquire product ion data across a precursor mass range of interest. The data acquisition cycle comprises performing, for each of a plurality of isolation windows having different mass ranges, steps of (i) isolating precursor ions within the mass range of the isolation window, (ii) fragmenting the isolated precursor ions to generate product ions, and (iii) mass analyzing the product ions. ... Thermo Finnigan Llc

10/05/17 / #20170282113

Gas chromatography columns with integrated ferrules

A capillary column includes a fused silica tubing and a polyimide coating over the fusing silica tubing. Additionally, the capillary column further includes a first plurality of integrated ferrules positioned along at least a first portion of the fused silica tubing and spaced apart from one another by a first fixed interval.. ... Thermo Finnigan Llc

09/07/17 / #20170256389

Ion beam mass pre-separator

An apparatus for separating ions includes an electrode arrangement having a length extending between first and second ends. The first end is configured to introduce a beam of ions into an ion transmission space of the arrangement. ... Thermo Finnigan Llc

08/10/17 / #20170227507

Apparatus and method for coupling tubing to chromatographic column

A method for coupling a tubing to a liquid chromatography column comprises: passing an end of the tubing through a coupling apparatus comprising: (i) at least one chamber; (ii) a first spring within the at least one chamber configured to transmit a spring force to the tubing; (iii) a second spring within the at least one chamber; and (iv) a deformable sealing member configured to receive a second force from the second spring; inserting the tubing end into a receptacle of an end fitting of the column; and moving the coupling apparatus towards the chromatography column such that the first spring urges the tubing into the receptacle whereby a pressure of the tubing end against the end fitting exceeds a maximum operating fluid pressure of the column and, further, whereby the second spring causes the deformable sealing member to form a fluid seal between the column and the receptacle.. . ... Thermo Finnigan Llc

08/03/17 / #20170221689

Ion separation and storage system

Ions provided from an ion source are separated ions into a plurality of different ion groups according to at least one ion property. At least some of the different ion groups are stored in an ion storage array, which comprises a plurality of independently operable storage cells, each storage cell being arranged to receive and store a different ion group. ... Thermo Finnigan Llc

07/20/17 / #20170207075

Ion transfer tube flow and pumping system load

A mass spectrometer system can include an ion source, a vacuum chamber; a mass analyzer within the vacuum chamber, a transfer tube between the ion source and the vacuum chamber, a transfer tube heater, and a vacuum pump. The mass spectrometer system can be configured to reduce the pump speed of the vacuum pump in response to receiving a transfer tube swap instruction; lower the temperature of the transfer tube to below a first threshold; operating the vacuum pump at the reduced pump speed while the transfer tube is replaced with a second transfer tube; heating the second transfer tube to a temperature above a pump down temperature; and increasing the pump speed of the vacuum pump after the temperature of the second transfer tube exceeds a second threshold.. ... Thermo Finnigan Llc

07/20/17 / #20170205426

Rapid mass spectrometry methods for antimicrobial susceptibility testing using top-down mass spectrometry

Methods and systems for rapid prediction and/or confirmation of antimicrobial susceptibility of a microorganism using top-down mass spectrometry, ion-ion chemistry, and a database with susceptibility, pathogenicity and antimicrobial resistance markers for sample characterization.. . ... Thermo Finnigan Llc

07/20/17 / #20170205425

Methods for top-down multiplexed mass spectral analysis of mixtures of proteins or polypeptides

Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (ptr) and real-time data analysis methods are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kda by removing charge and reducing the collisional cross section.. . ... Thermo Finnigan Llc

07/20/17 / #20170205424

Methods for mass spectrometric based characterization of biological molecules

Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (ptr) combined with higher-collision-energy dissociation (hcd) are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kda by removing charge, reducing the collisional cross section, and, in several cases, enhancing the sequence coverage obtained.. . ... Thermo Finnigan Llc

06/08/17 / #20170162372

Methods for mass spectrometry of mixtures of protein or polypeptides using proton transfer reaction

Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (ptr) are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kda by removing charge and reducing the collisional cross section.. . ... Thermo Finnigan Llc

06/08/17 / #20170162371

Methods and apparatus for tandem collision-induced dissociation cells

A method for operating a mass spectrometer so as to detect or quantify analytes, comprises: (a) identifying a selected-reaction-monitoring (srm) transition to be used for each respective analyte; (b) determining a time duration required for a fragmentation reaction corresponding to each identified transition to proceed to a threshold percentage of completion; and (c) for each analyte, performing the steps of (i) isolating ions corresponding to a precursor-ion mass-to-charge (m/z) ratio of the respective transition; (ii) fragmenting the respective isolated ions in one of two fragmentation cells or fragmentation cell portions; and (ii) mass analyzing for fragment ions corresponding to a product-ion m/z ratio of the respective transition, wherein, for each analyte, the fragmentation cell or fragmentation cell portion that is used for fragmenting the isolated ions is determined from the time duration determined for the respective analyte.. . ... Thermo Finnigan Llc

05/18/17 / #20170140913

Strong field photoionization ion source for a mass spectrometer

An ion source for a mass spectrometer comprises: an evacuated chamber having an interior receiving a gaseous sample effluent stream; a source of light pulses of pulse width 150 femtoseconds or less; a window of the evacuated chamber through which the light pulses pass into the evacuated chamber interior; one or more mirrors within the evacuated chamber disposed such that the light pulses are reflected from each of the one or mirrors such that the reflected pulses are caused to focus at one or more focal regions within the effluent stream within the evacuated chamber interior; and a pair of electrodes disposed at opposite sides of the one or more focal regions.. . ... Thermo Finnigan Llc

05/11/17 / #20170133215

High-resolution ion trap mass spectrometer

Techniques can increase the resolution and accuracy of mass spectra obtained using ion traps through the use of the actual shape of the ion trap peaks, which is a series of smaller ion ejection events. The peak shapes are identified as changing over a common period of the trapping signal and the excitation signal, at which point the peak shapes repeat. ... Thermo Finnigan Llc

05/11/17 / #20170131247

Minimal spanning trees for extracted ion chromatograms

A method for generating an extracted ion chromatogram (xic) from mass spectrometry data is disclosed. Mass spectrometry data are received comprised of a plurality of data points, each data point representing a measured ion intensity at a mass to charge ratio at a chromatographic retention time and these data are filtered to produce a filtered dataset. ... Thermo Finnigan Llc

05/11/17 / #20170131246

Systems and methods for ionization

A system for analyzing a sample includes a chromatographic device, an electrospray source, and a mass resolving device. The chromatographic device is configured to separate components of the sample as a function of retention time within a chromatographic column. ... Thermo Finnigan Llc

04/06/17 / #20170098536

Systems and methods for multipole operation

A method for identifying components of a sample includes providing a sample to an ion source and generating a plurality of ions from constituent components of the sample, applying a first rf waveform at a first rf amplitude to an ion trap with field resonances while directing the plurality of ions into the ion trap, and applying a second rf waveform at a second rf amplitude to the ion trap while focusing the plurality of ions towards the center of the ion trap along the longitudinal axis. The method further includes ejecting the plurality of ions from the ion trap into a mass analyzer, and using the mass analyzer to determine the mass-to-charge ratio of the ions.. ... Thermo Finnigan Llc

03/16/17 / #20170076928

Systems and methods for ion separation

A system for analyzing a sample includes a source configured to generate ions from constituent components of the sample; a mobility separation device, a plurality of ion channels, and a mass analyzer configured to determine the mass-to-charge ratio of the ions. The mobility device is configured to separate ions received from the source based on the mobility in a gas. ... Thermo Finnigan Llc

03/16/17 / #20170074827

Methods for operating a system comprising a coupled mass spectrometer and ion mobility spectrometer

A method of operating a system comprising a chromatograph, an ion source, a mass spectrometer having a mass analyzer and an ion mobility spectrometer interposed between the ion source and the mass analyzer, comprising: performing a first chromatographic and mass analysis of a sample while operating the ion mobility spectrometer in non-dispersive mode, wherein a respective ion-signal-acquisition time (at) and a corresponding loss-of-ion-signal time (lt) are identified for each detected m/z ratio that corresponds to a precursor-ion m/z ratio of interest; and performing a second chromatographic and mass analysis of the sample during which, for each identified at and lt, the corresponding respective precursor ion is fragmented to generate product ions and the product ions are detected by the mass analyzer, wherein the ion mobility spectrometer is operated in dispersive mode such that ions of said each respective precursor-ion species are preferentially transmitted therethrough spectrometer to the mass analyzer.. . ... Thermo Finnigan Llc

02/16/17 / #20170047209

Systems and methods for targeted top down discovery

A system for analyzing a sample includes a chromatographic device, a mass resolving device, and a data processor. The chromatographic device is configured to separate components of the sample using a chromatographic column. ... Thermo Finnigan Llc

01/26/17 / #20170023536

Modular multiple-column chromatography cartridge

A method for liquid chromatography comprises steps of: mixing a sample comprising a plurality of chemical constituents with a first solvent; transferring the solvent and the plurality of constituents to a first chromatographic column housed in a cartridge; chromatographically separating a sub-group of the plurality of constituents from unwanted constituents using the first chromatographic column; transferring the sub-group of the plurality of constituents from the first chromatographic column to a second column housed in the cartridge, the transferring effected by the flow of a second solvent; chromatographically separating, from one another, individual constituents of the sub-group of the plurality of constituents using the second chromatographic column; and transferring the separated individual constituents to a detector.. . ... Thermo Finnigan Llc

01/26/17 / #20170023534

Systems and methods for conserving carrier gas

A device for a gas chromatograph system includes an injector, a conduit assembly, a flow restrictor, and a pressure controller. The injector is connected to a carrier gas source and an auxiliary gas source. ... Thermo Finnigan Llc

01/12/17 / #20170010244

Method and system for decoupling a capillary column from a gas chromatography-mass spectrometry (gc-ms) system

A column-sealing tool is provided for use during decoupling of a capillary column from a gas chromatography-mass spectrometry (gc-ms) system. The column-sealing tool includes an engagement structure for removably securing the column-sealing tool within a high vacuum enclosure of the gc-ms system, at a location between a high vacuum end of a transfer line and a mass analyzer of the gc-ms system. ... Thermo Finnigan Llc








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