Dh Technologies Development Pte. Ltd.

Eth Zurich

Stephen Alexander Tate

Ronald Francis Bonner

Rudolf Aebersold

Lukas Reiter

Oliver Rinner

Pedro Jose Navarro Alvarez

Ludovic Gillet

Lyle Lorrence Burton

John Lawrence Campbell

Nic G Bloomfield

David Michael Cox

Chang Liu

Yves Le Blanc

Gordana Ivosev

Ignat V Shilov

Ron Bonner

Michael Murphy

Matthias Glueckmann

John R Burton

James Andrew Sherman

An ADE device identifies an identifiable sequence of one or more ejections from at least one sample using a different value or pattern of values for one or more ADE parameters. The identifiable one or more ejections are performed to produce one or more mass peaks that have a different feature value or pattern of feature values for one or more peak features than other mass peaks produced. Ejection times are stored. One or more detected peaks with the different feature values or pattern of feature values are identified as produced by the identifiable one or more ejections. A delay time is calculated from the time of the identifiable ejections and the time of the identified detected peaks and the peaks are aligned with samples using delay time, stored times, and order of the samples.

Identification of a first sample in a series of sequential samples

Systems and methods are disclosed for analyzing a sample using overlapping precursor isolation windows. A mass analyzer of a tandem mass spectrometer is instructed to select and fragment at least two overlapping precursor isolation windows across a precursor ion mass range of a sample using a processor. The tandem mass spectrometer includes a mass analyzer that allows overlapping precursor isolation windows across the mass range of the sample.

Data independent acquisition of product ion spectra and reference spectra library matching

A separation device is instructed to separate a compound from a sample over a time period. A mass spectrometer is instructed to measure a plurality of intensities of at least one ion of the separated compound over the time period, producing a chromatogram. At least one peak of the at least one ion is identified from the chromatogram using a peak-finding algorithm. Two or more different peak integration areas are calculated for the at least one peak by applying the peak-finding algorithm with two or more different values for at least one peak-finding parameter. Two or more plots of the at least one peak that each shows graphically a different peak integration area are displayed on a display device at the same time. In response, data is received from a user selection device that indicates user selection of one of the two or more plots.

Peak integration correction without parameter adjustment

A known compound and at least one adduct, modified form, or peptide of the known compound are separated from a sample mixture and analyzed. An XIC is calculated for each of M product ions of the known compound and L product ions of the at least one adduct, modified form, or peptide. A first XIC peak group is calculated from the M XICs and a second XIC peak group is calculated from the L XICs using curve subtraction. Representative first and second XIC peaks are selected for the two XIC peak groups. The retention time of the second XIC peak is shifted by an expected retention time difference found from a database. The retention time of the first XIC peak is verified as the retention time of the known compound if the difference of the retention times of the first and second XIC peaks is within a threshold.

Identification and scoring of related compounds in complex samples

A system and method is provided for monitoring a production process. In some aspects, the system may include an aseptic sampling device in fluidic connection with a process fluid, the aseptic sampling device operative to collect one or more samples from the process stream. A pretreatment device may be included to receive and pretreat the one or more samples. An analyzer is operative to analyze the pretreated samples and to produce one or more mass spectrometry (MS) spectra. A classifier receives and classifies the one or more MS spectra to provide a measure of product quality of the process fluid corresponding to the sampling location and time of sampling.

System and method for monitoring a production process

Systems and methods are provided for identifying a precursor ion without using any a priori precursor ion information. In one method, a sample is analyzed using a tandem mass spectrometer, producing at least one measured product ion spectrum from a precursor mass-to-charge ratio range. The at least one measured product ion spectrum are received. A subset of measured product ions is selected from the at least one measured product ion spectrum. A list of candidate compounds is created by searching a dictionary of potential compounds that includes one or more predicted product ions for each of the potential compounds using the subset of measured product ions. A candidate compound on the list is selected as the identified compound. In another method, the measured product ions are assumed to correspond to shortened forms of the peptide and a protein database is searched for shortened forms of the peptide.

Systems and methods for identifying compounds from MS/MS data without precursor ion information

A plurality of measured product ion spectra is produced using a DIA tandem mass spectrometry method. One or more product ions are retrieved from a spectral library of known compounds or one or more theoretical product ions are calculated for the known compounds of a database. For each known or theoretical product ion, an XIC is calculated from the measured product ion spectra. Measured XIC peaks above a threshold intensity are grouped for the known compounds producing a subset of known compounds. Known or theoretical retention times are retrieved or calculated for the subset of known compounds. A regression function is calculated to correct the known or theoretical retention times using the known or theoretical retention times of the subset of known compounds as the independent variables and the measured retention times of the measured XIC peak groups of the subset of known compounds as the dependent variables.

Automated spectral library retention time correction

A plurality of measured product ion spectra are produced using a DIA tandem mass spectrometry method. One or more product ions are retrieved from a spectral library of known compounds or one or more theoretical product ions are calculated for the known compounds of a database. The one or more product ions or one or more theoretical product ions for each known compound are compared to the measured product ion spectra to identify one or more known compounds in the sample. A database of related known compounds is searched using one or more known compounds, producing one or more matching related compounds and one or more product ions for each related compound. The one or more product ions for each related compound are compared to the measured product ion spectra to identify one or more related compounds in the sample.

Results dependent analysis&#x2014;iterative analysis of SWATH data

A plurality of product ion spectra measured over plurality of cycles for each precursor ion mass selection window of two or more precursor ion mass selection windows are received from a tandem mass spectrometer. A product ion extracted ion chroatograms (XIC) is calculated for each precursor ion mass selection window of the two or more precursor ion mass selection windows from the plurality of product ion spectra for each precursor ion mass selection window. Two or more product ion XICs are produced. A two-dimensional binary bit matrix is generated to represent each product ion XIC of the two or more product ion XICs. For each XIC of the two or more product ion XICs, the binary bit matrix is separately initialized with binary values calculated from each XIC and the initialized binary bit matrix is compared with stored information about known compounds to identify known compounds of each XIC.

Rapid scoring of LC-MS/MS peptide data

Systems and methods are used to analyze a sample using variable mass selection window widths. A tandem mass spectrometer is instructed to perform at least two fragmentation scans of a sample with different mass selection window widths using a processor. The tandem mass spectrometer includes a mass analyzer that allows variable mass selection window widths. The selection of the different mass selection window widths can be based on one or more properties of sample compounds. The properties may include a sample compound molecular weight distribution that is calculated from a molecular weight distribution of expected compounds or is determined from a list of molecular weights for one or more known compounds. The tandem mass spectrometer can also be instructed to perform an analysis of the sample before instructing the tandem mass spectrometer to perform the at least two fragmentation scans of the sample.

Systems and methods for using variable mass selection window widths in tandem mass spectrometry

A system is disclosed for identifying precursor ions originating from an ion source device. A mass filter filters an ion beam by using a series of overlapping precursor ion mass selection windows across the precursor ion mass range. A mass analyzer analyzes the precursor ions of each precursor ion mass selection window of the series, producing a plurality of precursor ion spectra for the precursor ion mass range. A precursor ion is selected from the spectra. The intensities for the selected precursor ion are retrieved from the spectra and a trace is produced that describes how the intensity of the selected precursor ion varies with the location of the precursor ion mass selection window. The selected precursor ion is identified as a precursor ion originating from the ion source device if the trace includes a nonzero intensity for the m/z value of the selected precursor ion.

Physical isolation of adducts and other complicating factors in precursor ion selection for IDA

A system is disclosed for identifying a precursor ion of a product ion in a scanning DIA experiment. A precursor ion mass selection window is scanned across a precursor ion mass range of interest, producing a series of overlapping windows across the precursor ion mass range. Each overlapping window is fragmented and mass analyzed, producing a plurality of product ion spectra for the mass range. A product ion is selected from the spectra. Intensities for the selected product ion are retrieved for at least one scan across the mass range producing a trace of intensities versus precursor ion m/z. A matrix multiplication equation is created that describes how one or more precursor ions correspond to the trace for the selected product ion. The matrix multiplication equation is solved for one or more precursor ions corresponding to the selected product ion using a numerical method.

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Barrie, Canada

Stephen Alexander Tate