Abstract: Methods and systems for mass spectrometry are disclosed. In one example, a method comprises: receiving, by a mass spectrometer via a sampling system operably connected thereto, at least one sample containing at least one known compound; modulat-ing at least one instrument parameter of the mass spectrometer through a plurality of instrument parameter values; analyzing the at least one sample while applying each of the plurality of instrument parameter values; acquiring a plurality of mass spectral (MS) datasets each corresponding to one of the applied plurality of instrument parameter values; encoding each of the plurality of MS datasets to generate a corresponding plurality of MS results each corresponding to one of the applied instrument parameter values; and compiling and storing the MS datasets and MS results in a spectral library in association with the applied instrument parameter values.

Abstract: A mass range is fragmented and mass analyzed using n samples, producing measurements in n dimensions. Two clustering algorithms are applied to the measurements, producing two sets of clusters, and compounds in the sets are identified. Two or more compounds found in a cluster of both sets are identified. The two or more compounds are compared to groups of compounds related to a biological process to identify a group that includes the two or more compounds. An additional compound is selected from the group. The two sets are reanalyzed to identify the compound in the sets. A co-occurrence matrix is calculated that quantifies the co-occurrence of the compound and each of the two or more compounds in the sets. If no co-occurrence quantity for the compound and each of the two or more compounds in the matrix is below a threshold, the two or more compounds are verified.

Abstract: Systems and methods are disclosed for performing a DDA mass spectrometry experiment. A precursor ion survey scan of a mass range is performed to generate a precursor ion peak list. A series of steps are performed for each precursor ion peak of the peak list. A peak mass range including the precursor ion peak is selected. A precursor ion mass selection window with a width smaller than the peak mass range is canned across the peak mass range in overlapping steps, producing a series of overlapping windows across the peak mass range. Each overlapping precursor ion mass selection window of the series is fragmented. Product ions produced from each overlapping precursor ion mass selection window of the series are mass analyzed, producing a product ion spectrum for each overlapping precursor ion mass selection window of the series and a plurality of product ion spectra for the peak.

Abstract: 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.

Abstract: During each time cycle, a precursor ion transmission window is stepped in k overlapping steps that are ?m m/z apart entirely across a mass range from a starting mlm/z. The window is stepped n?1 more times starting at n?1 different offsets from ml between ml and ml+?m. A total of n scans of the mass range. A total of k×n product ion spectra are produced that are a function of precursor ion m/z for each time cycle. A product ion is selected from the spectra. For at least one time cycle, an intensity of the product ion as a function of precursor ion m/z is reconstructed with a resolving power greater than ?m by combining intensities of the product ion measured during each of the n scans using a linear reconstruction algorithm, such as Drizzle.

Abstract: 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.

Abstract: An uncertainty weighted average of the equalized amounts of two or more quantifier ions is calculated from a quantitation experiment itself. n known i ions of a compound are mass analyzed over time in each of m different samples, producing n XIC peaks for each of the m samples. A reference ion j is selected that is a j ion of the n i ions or a hypothetical ion j. A ratio r(j,i) of a peak area of the j ion to a peak area of each ion of the n i ions is calculated for each of the m samples, producing m r(j,i) ratios for each of the n i ions. An expected ratio rq(j,i) is calculated for each ion of the n i ions from the m r(j,i) ratios for each of the n i ions. For each sample, the uncertainty weighted average is calculated using rq(j,i).

Abstract: 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.

Abstract: A compound is separated or introduced from a sample at a plurality of different times. The compound is ionized, producing an ion beam. The compound is selected and mass analyzed or the compound is selected, fragmented, and fragments of the compound are analyzed from the ion beam at the plurality of different times, producing a plurality of mass spectra. An XIC is calculated for the compound using the plurality of mass spectra. A chemical structure of the compound received in notation form is converted to a numerical vector using a processing algorithm operable to convert the notation form to the numerical vector. A plurality of peak shape parameters is calculated for the compound using the numerical vector and a machine trained model. A peak of the XIC is identified as a peak of the compound using the plurality of peak shape parameters and optionally a peak integration algorithm.

Abstract: 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.

Abstract: 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 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: A device that produces charged droplets whose composition is optimized for the creation of ions by electro spray composed of: a transport device that is operative to transfer sample components from a liquid sample to a processing chamber, a flowing stream of liquid through the processing chamber into which the samples are deposited, a controller mechanism operative to control the amount of sample transferred, a transport tube through which the flowing liquid containing the sample is directed to an electro spray emitter with a high electric field at the exit, a flow of expanding gas surrounding the electro spray emitter creating a pressure drop at the exit, and, a mass spectrometer for measuring the number of ions produced from the charged droplets emanating from the emitter; wherein the dilution of the sample in the processing chamber and transport fluid is from 100 to 10,000-fold.

Abstract: 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.

Abstract: 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.

Abstract: 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.