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: 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: Techniques are described for matching a precursor ion with one or more related product ions, including providing a plurality of input data sets obtained from a plurality of injections, each of the plurality of input data sets including a same precursor ion and one or more product ions, normalizing the plurality of input data sets in accordance with a single retention time for the precursor ion, for each of the plurality of input data sets, determining which product ions are within a predetermined retention time window with respect to the single retention time for the precursor ion, and if a product ion is within the predetermined retention time window in at least one of the plurality of input data sets, determining that the product ion is related to the precursor ion having the single retention time

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 system and method for mass analysis where a sample (102) is separated in a liquid chromatograph (104), and subsequently analyzed in a mass spectrometer (112).

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: 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: 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 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: 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 arc 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 system and method for mass analysis where a sample (102) is separated in a liquid chromatograph (104), and subsequently analyzed in a mass spectrometer (112).

Abstract: A compact high-performance mass spectrometer includes an ion source, an ion filter, a collision cell, a fragment filter, and an ion detector, along with one or more ion deflectors and one or more gas removal rings. An ion deflector allows a straight ion filter and a straight collision cell to be coupled in a folded configuration to make a compact design without the loss of performance associated with the use of curved quadrupole components. A gas removal ring, located proximate to an ion path aperture of the collision cell, allows an ion path aperture to be large for high sensitivity while minimizing performance degradation associated with the tendency of collision cell gas to escape via the collision cell ion path apertures to enter the high vacuum region and the detector.