Abstract: A method for analyzing chemicals includes fractionating a complex sample into at least two sample portions that each include portions of two polypeptides though in different concentration ratios, digesting and performing LC/MS on each of the sample portions, and associating precursor ions observed via LC/MS with their corresponding polypeptide in response to LC/MS-provided intensity data. 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: 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: A chemical processing apparatus includes a fragmentation device that includes a linear set of stacked electrodes and a voltage control module that forms DC potential wells of opposite polarity for mutual confinement of opposite polarity ions. A method of protein analysis includes confining positive peptide ions and negatively charged reagent anions in, respectively, first and second DC potential wells in a fragmentation device, mixing the ions, in the fragmentation device, and analyzing ion fragments formed in the mixture.

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: 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 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: 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: 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: 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: 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: 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: A method for analyzing chemicals includes fractionating a complex sample into at least two sample portions that each include portions of two polypeptides though in different concentration ratios, digesting and performing LC/MS on each of the sample portions, and associating precursor ions observed via LC/MS with their corresponding polypeptide in response to LC/MS-provided intensity data. 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: 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: 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: 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 a control unit in communication with the chromatography module and the mass-spectrometry module.

Abstract: A method (100) for analyzing chemicals includes fractionating a complex sample into at least two sample portions that each includes portions 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: A method (100) for performing chemical analyses includes digesting a reference sample to obtain precursors associated with a peptide in the sample (110), separating the precursors to determine values associated with retention times of the separated precursors (120), ionizing the separated precursors to form precursor ions (130), mass analyzing the precursor ions to determine values associated with mass and with ion intensity (140), and storing a <fcfile of the polypeptide defined by the determined values (150). A subject sample is analyzed (160), and the polypeptide is detected in the subject sample in response to a match between subject-sample and profile values. An apparatus (900) for performing chemical analyses includes a chromatography module (904), a mass-spectrometry module (912), and a computer module (926).

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: 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.