Abstract: A method of preparing a liquid protein sample for proteome analysis is provided. The method comprises pumping a liquid protein sample into a heated tubing, wherein the liquid protein sample comprises a plurality of portions; incubating the liquid protein sample in the heated tubing, wherein an incubation condition for a first portion of the sample is different to an incubation condition for a second portion of the sample; and pumping the liquid protein sample out of the heated tubing.

Abstract: An accelerator includes a memory, a compute zone to receive an encrypted workload downloaded from a tenant application running in a virtual machine on a host computing system attached to the accelerator, and a processor subsystem to execute a cryptographic key exchange protocol with the tenant application to derive a session key for the compute zone and to program the session key into the compute zone. The compute zone is to decrypt the encrypted workload using the session key, receive an encrypted data stream from the tenant application, decrypt the encrypted data stream using the session key, and process the decrypted data stream by executing the workload to produce metadata.

Abstract: A mass spectrometry method comprises: providing a multiplexed sample comprising a mixture of biomolecule-containing samples respectively tagged with mass tags; acquiring MS2 spectra by data-dependent acquisition (DDA) of the multiplexed sample or another mass tagged mixture of the samples during chromatographic elution; acquiring MS2 spectra by data-independent acquisition (DIA) during the elution; forming a spectral library from the DDA MS2 spectra comprising a plurality of the MS2 spectra and the biomolecule retention times; matching fragment-ion peaks in the DIA MS2 spectra to fragment-ion peaks in the MS2 library spectra to find matched biomolecules; determining a total abundance for each matched biomolecule from the DIA MS2 spectra at each of a plurality of retention times; determining abundances of respective reporter ions from the DIA MS2 spectra at the plurality of retention times; and deconvoluting relative abundances of the biomolecules in each respectively tagged biomolecule-containing sample based

Abstract: An accelerator includes a memory, a compute zone to receive an encrypted workload downloaded from a tenant application running in a virtual machine on a host computing system attached to the accelerator, and a processor subsystem to execute a cryptographic key exchange protocol with the tenant application to derive a session key for the compute zone and to program the session key into the compute zone. The compute zone is to decrypt the encrypted workload using the session key, receive an encrypted data stream from the tenant application, decrypt the encrypted data stream using the session key, and process the decrypted data stream by executing the workload to produce metadata.

Abstract: A mass spectrometry method comprises: providing a multiplexed sample comprising a mixture of biomolecule-containing samples respectively tagged with mass tags; acquiring MS2 spectra by data-dependent acquisition (DDA) of the multiplexed sample or another mass tagged mixture of the samples during chromatographic elution; acquiring MS2 spectra by data-independent acquisition (DIA) during the elution; forming a spectral library from the DDA MS2 spectra comprising a plurality of the MS2 spectra and the biomolecule retention times; matching fragment-ion peaks in the DIA MS2 spectra to fragment-ion peaks in the MS2 library spectra to find matched biomolecules; determining a total abundance for each matched biomolecule from the DIA MS2 spectra at each of a plurality of retention times; determining abundances of respective reporter ions from the DIA MS2 spectra at the plurality of retention times; and deconvoluting relative abundances of the biomolecules in each respectively tagged biomolecule-containing sample based

Abstract: The present disclosure provides a method and apparatus for improvements of sample throughput in proteome analysis by mass spectrometry, by combining multiple non-overlapping isoelectric focusing separations.

Abstract: A method of quantifying analytes from mass spectral data, comprising: obtaining a first set of mass spectral data from a first set of analytes eluted from a chromatography column; obtaining a second set of mass spectral data from a second set of analytes eluted from a chromatography column; determining apparent abundances of analytes in each data set; selecting a target analyte and determining localized neighboring analytes by their locality to the target analyte with respect to retention time; determining a locally corrected abundance of the target analyte based on differences between the first and second data sets in the apparent abundance of the localized neighboring analytes; and quantifying the target analyte based on its corrected abundance. A majority of the neighboring analytes are typically substantially unchanged in actual abundance between the first and second data sets and can be used for aligning the abundances between the data sets.

Abstract: A method of identifying precursor ion species from their fragments comprises obtaining mass spectra of a plurality of precursor ion species and their fragments to high mass accuracy. The fragment mass spectrum, obtained from fragmentation of multiple precursor ion species, is then scanned it identify pairs of fragments whose combined mass matches the mass of one of the precursor ion species. Once pairs of fragment ion shave been matched to precursor ions, the composite fragment ion spectrum is broken down into portions, one per fragment pair. Analysis continues until no further pairs are identified. A simplified fragment ion spectrum is then reconstructed for each precursor sample ion by stitching together the broken down sections of the composite fragment spectrum. The resultant reconstructed, simplified fragment spectra are sent to a search engine which returns a score—sorted list of likely candidates for each synthetic fragment ion spectrum.

Abstract: A method of identifying precursor ion species from their fragments comprises obtaining mass spectra of a plurality of precursor ion species and their fragments to high mass accuracy. The fragment mass spectrum, obtained from fragmentation of multiple precursor ion species, is then scanned it identify pairs of fragments whose combined mass matches the mass of one of the precursor ion species. Once pairs of fragment ion shave been matched to precursor ions, the composite fragment ion spectrum is broken down into portions, one per fragment pair. Analysis continues until no further pairs are identified. A simplified fragment ion spectrum is then reconstructed for each precursor sample ion by stitching together the broken down sections of the composite fragment spectrum. The resultant reconstructed, simplified fragment spectra are sent to a search engine which returns a score—sorted list of likely candidates for each synthetic fragment ion spectrum.

Abstract: A method of identifying precursor ion species from their fragments comprises obtaining mass spectra of a plurality of precursor ion species and their fragments to high mass accuracy. The fragment mass spectrum, obtained from fragmentation of multiple precursor ion species, is then scanned it identify pairs of fragments whose combined mass matches the mass of one of the precursor ion species. Once pairs of fragment ion shave been matched to precursor ions, the composite fragment ion spectrum is broken down into portions, one per fragment pair. Analysis continues until no further pairs are identified. A simplified fragment ion spectrum is then reconstructed for each precursor sample ion by stitching together the broken down sections of the composite fragment spectrum. The resultant reconstructed, simplified fragment spectra are sent to a search engine which returns a score-sorted list of likely candidates for each synthetic fragment ion spectrum.

Abstract: A collision cell for a mass spectrometer arranged to receive ions for fragmentation in a chamber and comprising an activation ion generator configured to irradiate the received ions with activation ions of the same polarity as the received ions. The activation ion generator is preferably a plasma generator, configured to generate a plasma comprising the activation ions.

Abstract: A method of quantifying analytes from mass spectral data, comprising: obtaining a first set of mass spectral data from a first set of analytes eluted from a chromatography column; obtaining a second set of mass spectral data from a second set of analytes eluted from a chromatography column; determining apparent abundances of analytes in each data set; selecting a target analyte and determining localised neighboring analytes by their locality to the target analyte with respect to retention time; determining a locally corrected abundance of the target analyte based on differences between the first and second data sets in the apparent abundance of the localised neighboring analytes; and quantifying the target analyte based on its corrected abundance. A majority of the neighboring analytes are typically substantially unchanged in actual abundance between the first and second data sets and can be used for aligning the abundances between the data sets.

Abstract: A collision cell for a mass spectrometer arranged to receive ions for fragmentation in a chamber and comprising an activation ion generator configured to irradiate the received ions with activation ions of the same polarity as the received ions. The activation ion generator is preferably a plasma generator, configured to generate a plasma comprising the activation ions.

Abstract: A method of identifying precursor ion species from their fragments comprises obtaining mass spectra of a plurality of precursor ion species and their fragments to high mass accuracy. The fragment mass spectrum, obtained from fragmentation of multiple precursor ion species, is then scanned it identify pairs of fragments whose combined mass matches the mass of one of the precursor ion species. Once pairs of fragment ion shave been matched to precursor ions, the composite fragment ion spectrum is broken down into portions, one per fragment pair. Analysis continues until no further pairs are identified. A simplified fragment ion spectrum is then reconstructed for each precursor sample ion by stitching together the broken down sections of the composite fragment spectrum. The resultant reconstructed, simplified fragment spectra are sent to a search engine which returns a score—sorted list of likely candidates for each synthetic fragment ion spectrum.

Abstract: A method of identifying precursor ion species from their fragments comprises obtaining mass spectra of a plurality of precursor ion species and their fragments to high mass accuracy. The fragment mass spectrum, obtained from fragmentation of multiple precursor ion species, is then scanned it identify pairs of fragments whose combined mass matches the mass of one of the precursor ion species. Once pairs of fragment ion shave been matched to precursor ions, the composite fragment ion spectrum is broken down into portions, one per fragment pair. Analysis continues until no further pairs are identified. A simplified fragment ion spectrum is then reconstructed for each precursor sample ion by stitching together the broken down sections of the composite fragment spectrum. The resultant reconstructed, simplified fragment spectra are sent to a search engine which returns a score-sorted list of likely candidates for each synthetic fragment ion spectrum.

Abstract: A measuring cell of an ICR mass spectrometer and a method of operating a measuring cell of the ICR mass spectrometer. The method and system trap ions in a first compartment of the ICR measuring cell by generating an electric potential well in the direction of the magnetic field with a minimum of the electric potential well located inside the first compartment. The method and system excite cyclotron motion of the ions trapped in the first compartment. The method and system transfer at least a part of the excited ions from the first compartment to a second compartment of the ICR measuring cell by displacement of a position of the minimum of the electric potential well from the first compartment to the second compartment.

Abstract: The invention relates to acquisition methods for fragment ion spectra of biopolymer molecules in tandem mass spectrometers which are coupled to separation devices. The invention provides a real-time method for calculating a quality coefficient for each fragment ion spectrum. The quality coefficient indicates whether the fragment ion spectrum can be used successfully for identifying the biopolymer molecule or whether it should be acquired once more, possibly with other acquisition parameters.

Abstract: A measuring cell of an ICR mass spectrometer and a method of operating a measuring cell of the ICR mass spectrometer. The method and system trap ions in a first compartment of the ICR measuring cell by generating an electric potential well in the direction of the magnetic field with a minimum of the electric potential well located inside the first compartment. The method and system excite cyclotron motion of the ions trapped in the first compartment. The method and system transfer at least a part of the excited ions from the first compartment to a second compartment of the ICR measuring cell by displacement of a position of the minimum of the electric potential well from the first compartment to the second compartment.

Abstract: A method of identifying precursor ion species from their fragments comprises obtaining mass spectra of a plurality of precursor ion species and their fragments to high mass accuracy. The fragment mass spectrum, obtained from fragmentation of multiple precursor ion species, is then scanned it identify pairs of fragments whose combined mass matches the mass of one of the precursor ion species. Once pairs of fragment ion shave been matched to precursor ions, the composite fragment ion spectrum is broken down into portions, one per fragment pair. Analysis continues until no further pairs are identified. A simplified fragment ion spectrum is then reconstructed for each precursor sample ion by stitching together the broken down sections of the composite fragment spectrum. The resultant reconstructed, simplified fragment spectra are sent to a search engine which returns a score-sorted list of likely candidates for each synthetic fragment ion spectrum.

Abstract: An ion cyclotron resonance cell has at least one trapping electrode comprised of electrically isolated sections that are used for the detection of an induced ion image signal. Such an arrangement increases the sensitivity of image signal detection without a significant increase in the amplitude of parasitic harmonics. When a multielectrode detection arrangement is used, the resolving power of an analyzer incorporating such a cyclotron resonance cell multiplies without a corresponding sensitivity loss.