Abstract: A method of preparing a liquid mixture for use in a liquid chromatography system is provided. The mixture comprises one or more acids, one or more bases, one or more salts, and one or more solvents, and the method comprises the steps of: i) calculating pH and/or salt concentration at a particular time t from a user-determined gradient function; and ii) based on the values obtained in step (i), calculating percent acid, percent base, percent salt and percent solvent in the liquid mixture at time t. A liquid chromatography system incorporating such method is also provided.

Abstract: A liquid chromatography system includes an autosampler with an injector valve by which a sample at low pressure within a sample loop is introduced into a high-pressure solvent mixture stream. A solvent delivery system includes a pump in fluidic communication with the injector valve of the autosampler to deliver the solvent mixture stream thereto. The solvent delivery system further comprises a processor that calculates a number of strokes of the pump needed to deliver the solvent mixture stream to the injector valve of the autosampler. The processor counts strokes of the pump during delivery of the solvent mixture stream. In response to a stroke count equaling the calculated number of strokes, the processor signals the autosampler to switch the injector valve to introduce the sample to the solvent mixture stream during a pump transfer period within which the pump performs pressure control to compensate for a drop in pressure.

Abstract: A liquid chromatography system includes an autosampler that prepares a sample for introduction to a solvent stream and a solvent delivery system that delivers a solvent stream to the autosampler. Delivery of the solvent stream occurs in parallel with the autosampler's pre-injection operations. The autosampler starts pre-injection operations to make the sample ready for injection into the mixture stream, and the solvent delivery system starts delivery of a solvent stream to the autosampler. The start of the solvent stream delivery is coordinated with the start of the pre-injection operations such that the solvent stream arrives at the autosampler approximately coincident with when the autosampler completes the pre-injection operations, making the sample ready for injection.

Abstract: LC/MS data generated by an LC/MS system is analyzed to determine groupings of ions associated with originating molecules. Ions are grouped initially according to retention time, for example, using retention time or chromatographic peaks in mass chromatograms. After initial groupings are determined based on retention time, ion peak shapes are compared to determine whether ions should be excluded. Ions having peak shapes not matching other ions, or alternatively a reference peak shape, are excluded from the group.

Abstract: LC/MS data generated by an LC/MS system is analyzed to determine groupings of ions associated with originating molecules. Ions are grouped initially according to retention time, for example, using retention time or chromatographic peaks in mass chromatograms. After initial groupings are determined based on retention time, ion peak shapes are compared to determine whether ions should be excluded. Ions having peak shapes not matching other ions, or alternatively a reference peak shape, are excluded from the group.

Abstract: In complex separations, more than one entity may have the same molecular weight, to within the ability of an instrument to distinguish. Accurate mass measurements are used in light of the previously unknown regularities in retention time to determine a retention time (N pairs of values (tiB, tiBref)) (506). The retention time map allows a reference retention time to be assigned to each entity in a separation. The reference retention times, together with accurate mass measurements, can then be used to track and to compare entities (704,708) between separations.

Abstract: A method for matching a precursor ion with one or more related product ions includes providing input data sets obtained from sample injections, each of the data sets including a precursor ion and one or more product ions, normalizing the input data sets in accordance with a single retention time for the precursor ion, determining which product ions are within a predetermined retention time window with respect to the single retention time, and, if a product ion is within the predetermined retention time window for a specified number of the input data sets, determining that the product ion is related to the precursor having the single retention time. An apparatus for analyzing a sample includes a chromatography module, a mass-spectrometry module in communication with the chromatography module, and control unit in communication with the chromatography module and the mass-spectrometry module.

Abstract: Embodiments of the present invention are directed to apparatus and methods for performing mass spectrometry. Data pair information is subjected to an ion audit process in which data pair information that relates to scored compounds is subtracted from the data pair information. The depleted information more readily reveals data pair information for compounds present with smaller signals.

Abstract: LC/MS data generated by an LC/MS system is analyzed to determine groupings of ions associated with originating molecules. Ions are grouped initially according to retention time, for example, using retention time or chromatographic peaks in mass chromatograms. After initial groupings are determined based on retention time, ion peak shapes are compared to determine whether ions should be excluded. Ions having peak shapes not matching other ions, or alternatively a reference peak shape, are excluded from the group.

Abstract: LC/MS data generated by an LC/MS system is analyzed to determine groupings of ions associated with originating molecules. Ions are grouped initially according to retention time, for example, using retention time or chromatographic peaks in mass chromatograms. After initial groupings are determined based on retention time, ion peak shapes are compared to determine whether ions should be excluded. Ions having peak shapes not matching other ions, or alternatively a reference peak shape, are excluded from the group.

Abstract: LC/MS data generated by an LC/MS system is analyzed to determine groupings of ions associated with originating molecules. Ions are grouped initially according to retention time, for example, using retention time or chromatographic peaks in mass chromatograms. After initial groupings are determined based on retention time, ion peak shapes are compared to determine whether ions should be excluded. Ions having peak shapes not matching other ions, or alternatively a reference peak shape, are excluded from the group.

Abstract: A method (100) for analyzing chemicals includes fractionating a complex sample into at least two sample portions that each includes potions of two polypeptides though in different concentration ratios, digesting and performing LC/MS on each of the sample portions (110, and associating precursor ions observed via LC/MS with their corresponding polypeptide in response to LC/MS provided intensity data (170). A set of precursor ions that has substantially similar intensity ratios in both sample portions is determined to be associated with the same polypeptide.

Abstract: Methods and apparatus for LC/IMS/MS analysis involve obtaining noisy raw data from a sample, convolving the data with an artifact-reducing filter, and locating, in retention-time, ion mobility, and mass-to-charge-ratio dimensions, one or more ion peaks of the convolved data.

Abstract: Absolute quantitation of protein in a sample is provided by comparing a sum or average of the N highest ionization intensities observed for peptides of a particular protein along with a calibration standard. The calibration standard can be in the form of a table generated by prior protein peptide analysis performed using one or more pre-determined proteins. The comparison is used to determine a corresponding absolute quantity of protein based on the observed sum or average of ionization intensities. A simple conversion factor can be applied to the calibration standard value to determine the absolute quantity of protein in the sample.

Abstract: Techniques are described for matching a precursor ion with one or more related product ions. Input data sets are obtained from a plurality of injections. Each of the input data sets includes a same precursor ion and one or more product ions. The input data sets are normalized in accordance with a single retention time for the precursor ion. For each input data set, it is determined which product ions are within a predetermined retention time window with respect to the single retention time for the precursor ion. If a product ion is within the predetermined retention time window in at least one of the input data sets, it is determined that the product ion is related to the precursor ion. An apparatus for analyzing a sample includes a chromatography module, a mass-spectrometry module, and a control unit.

Abstract: Protein identification in a complex sample begins by selecting a database having proteins likely to be in the sample. In-silico digestion is performed and a target peptide is selected from produced peptides. The masses of the Y- and B-ion fragments of the target peptide are determined. These masses are used to search previously obtained low- and high-energy AMRTs obtained from LC/MS analysis of the complex sample for masses on the list. Any mass observed in the data within a detection threshold are considered a hit. If enough hits accumulate in a given retention time, the target peptide is identified as being in the sample. The list of peptides identified in the complex sample can be used to identify the proteins present in the sample, track the chromatographic retention times of peptides between samples, and quantitate the peptides and proteins present in complex samples.

Abstract: A method of preparing a liquid mixture for use in a liquid chromatography system is provided. The mixture comprises one or more acids, one or more bases, one or more salts, and one or more solvents, and the method comprises the steps of: i) calculating pH and/or salt concentration at a particular time t from a user-determined gradient function; and ii) based on the values obtained in step (i), calculating percent acid, percent base, percent salt and percent solvent in the liquid mixture at time t. A liquid chromatography system incorporating such method is also provided.

Abstract: Methods and apparatus for LC/IMS/MS analysis involve obtaining noisy raw data from a sample, convolving the data with an artifact-reducing filter, and locating, in retention-time, ion mobility, and mass-to-charge-ratio dimensions, one or more ion peaks of the convolved data.

Abstract: Embodiments of the present invention are directed to a devices and methods for forming a desired miture of two or more fluids in a conduit. The devices and methods feature control means having error monitoring means and in response to an error event the control means organizes the packet-group of command signals to form at least one first error packet group. The error event occurs during the period of time in which the at least one error packet-group is received by a selectable value. The at least one error packet-group comprising an order or timing of first command signals and second commands signals to minimize deviation from the desired mixture in the flow of mixture-packets forming the desired mixture of two or more fluids in a conduit during the error event.

Abstract: A method for matching a precursor ion with one or more related product ions includes providing input data sets obtained from sample injections, each of the data sets including a precursor ion and one or more product ions, normalizing the input data sets in accordance with a single retention time for the precursor ion, determining which product ions are within a predetermined retention time window with respect to the single retention time, and, if a product ion is within the predetermined retention time window for a specified number of the input data sets, determining that the product ion is related to the precursor having the single retention time. An apparatus for analyzing a sample includes a chromatography module, a mass-spectrometry module in communication with the chromatography module, and control unit in communication with the chromatography module and the mass-spectrometry module.