Abstract: A variable data dependent acquisition/dynamic exclusion (vDDA/DE) method selects target m/z range utilizing a MS1 precursor topography map over the most recently acquired MS spectrum to identify the precursor m/z values and MS/MS acquisition parameters to improve the selection of the next data-dependent MS/MS acquisition. The topography used to define the next set of DDA scan events is defined by previous tandem MS scan events defined by precursor quadrupole isolation windows as well as all detected compounds contained within the specific tandem MS events. At least some of the parameters used for MS/MS data acquisition are dynamic so as to exhaustively sample the user specified MS mass range with MS/MS information. These parameters include the quadrupole MS isolation width and symmetry around the targeted m/z value. Using this approach, a greater proportion of the precursor m/z space is effectively and efficiently sampled per chromatographic peak width.

Abstract: Embodiments are directed to methods for representing cell content of a tissue sample. One method includes identifying a pixel in a digital image of a tissue sample. The identified pixel is mapped to a portion of the tissue sample. A first data set is accessed representing a genomics analysis of nucleic acids that are separated from tissue proteins in the tissue sample. A second data set is also accessed representing a proteomic analysis of proteins that were separated from the nucleic acids of the tissue sample. The data sets are mapped to a renderable attribute, so that the renderable attribute has a specified value based on the mapped data sets. Then, a portion of a representation is rendered for the identified pixel, according to the specified value of the renderable attribute. The representation includes an indication of how the separated nucleic acids and proteins are distributed within the tissue sample.

Abstract: A variable data dependent acquisition/dynamic exclusion (vDDA/DE) method selects target m/z range utilizing a MS1 precursor topography map over the most recently acquired MS spectrum to identify the precursor m/z values and MS/MS acquisition parameters to improve the selection of the next data-dependent MS/MS acquisition. The topography used to define the next set of DDA scan events is defined by previous tandem MS scan events defined by precursor quadrupole isolation windows as well as all detected compounds contained within the specific tandem MS events. At least some of the parameters used for MS/MS data acquisition are dynamic so as to exhaustively sample the user specified MS mass range with MS/MS information. These parameters include the quadrupole MS isolation width and symmetry around the targeted m/z value. Using this approach, a greater proportion of the precursor m/z space is effectively and efficiently sampled per chromatographic peak width.

Abstract: Provided herein are methods for determining the ratio of one or more isoforms of a protein in a sample.

Abstract: Methods are described for monitoring the amounts of PTH variants in a biological sample by digesting the sample to produce surrogate peptides specific to the targeted PTH variants, and detecting and quantifying the surrogate peptides by selective reaction monitoring (SRM) mass spectrometry, using a set of precursor-to-product ion transitions optimized for sensitivity and selectivity. The PTH variants, or a portion thereof, may be concentrated in the sample by means of immunoaffinity capture or other suitable technique. The mass spectrometric method described herein enables the concurrent measurement of peptides representative of a plurality of targeted PTH variants in a single assay.

Abstract: Methods are described for monitoring the amounts of PTH variants in a biological sample by digesting the sample to produce surrogate peptides specific to the targeted PTH variants, and detecting and quantifying the surrogate peptides by selective reaction monitoring (SRM) mass spectrometry, using a set of precursor-to-product ion transitions optimized for sensitivity and selectivity. The PTH variants, or a portion thereof, may be concentrated in the sample by means of immunoaffinity capture or other suitable technique. The mass spectrometric method described herein enables the concurrent measurement of peptides representative of a plurality of targeted PTH variants in a single assay.

Abstract: A method for determining a time of elution of a peptide of interest from a liquid chromatography column includes a step of obtaining chromatographic data for each of a plurality of candidate fragment ions of the peptide of interest. A time along a common chromatographic time is scale determined corresponding to maximum overlay of the ion signals measured for each of the plurality of candidate fragment ions. Finally, the determined time is assigned as the time of elution of the peptide of interest from the liquid chromatography column. In particular, the chromatographic data is acquired during selective reaction monitoring of an eluate from the liquid chromatography column containing the peptide of interest. The chromatographic data includes ion signals measured along the common chromatographic time scale for each of the plurality of candidate fragment ions.

Abstract: Methods are disclosed for rapidly and reliably differentiating between ischemic and hemorrhagic stroke events in a human patient. The methods include obtaining a biological sample, such as blood serum, and analyzing the sample or a derivative thereof by mass spectrometry to measure the amount of one or more targeted proteins differentially present and ischemic and hemorrhagic stroke patients. The analysis may include proteolytic digestion of the biological sample and selective reaction monitoring (SRM) tandem mass spectrometry of the digested sample to determine the amounts of surrogate peptides corresponding to the targeted proteins.

Abstract: Methods are described for monitoring the amounts of PTH variants in a biological sample by digesting the sample to produce surrogate peptides specific to the targeted PTH variants, and detecting and quantifying the surrogate peptides by selective reaction monitoring (SRM) mass spectrometry, using a set of precursor-to-product ion transitions optimized for sensitivity and selectivity. The PTH variants, or a portion thereof, may be concentrated in the sample by means of immunoaffinity capture or other suitable technique. The mass spectrometric method described herein enables the concurrent measurement of peptides representative of a plurality of targeted PTH variants in a single assay.

Abstract: A method for determining a time of elution of a peptide of interest from a liquid chromatography column includes a step of obtaining chromatographic data for each of a plurality of candidate fragment ions of the peptide of interest. A time along a common chromatographic time is scale determined corresponding to maximum overlay of the ion signals measured for each of the plurality of candidate fragment ions. Finally, the determined time is assigned as the time of elution of the peptide of interest from the liquid chromatography column. In particular, the chromatographic data is acquired during selective reaction monitoring of an eluate from the liquid chromatography column containing the peptide of interest. The chromatographic data includes ion signals measured along the common chromatographic time scale for each of the plurality of candidate fragment ions.

Abstract: A method for determining a time of elution of a peptide of interest from a liquid chromatography column includes a step of obtaining chromatographic data for each of a plurality of candidate fragment ions of the peptide of interest. A time along a common chromatographic time is scale determined corresponding to maximum overlay of the ion signals measured for each of the plurality of candidate fragment ions. Finally, the determined time is assigned as the time of elution of the peptide of interest from the liquid chromatography column. In particular, the chromatographic data is acquired during selective reaction monitoring of an eluate from the liquid chromatography column containing the peptide of interest. The chromatographic data includes ion signals measured along the common chromatographic time scale for each of the plurality of candidate fragment ions.

Abstract: The present invention relates to biomarkers in maternal serum samples and methods for predicting whether a fetus has Trisomy 21 during the first trimester of pregnancy based on the differential expression of a combination, or subcombination, of the same.

Abstract: Methods for selecting a set of SRM transitions for a peptide of interest include selecting a first transition based on sensitivity criteria and selecting at least a second transition based on selectivity criteria. A determination of the uniqueness of the first transition combined with the at least a second transition is made. When the combination of the first transition and the at least a second transition is determined to be unique to the peptide of interest, a sample containing the peptide of interest is subjected to a SRM workflow by monitoring the first transition and the second transition. Also described is an apparatus for carrying out the methods.

Abstract: A method for determining a time of elution of a peptide of interest from a liquid chromatography column includes a step of obtaining chromatographic data for each of a plurality of candidate fragment ions of the peptide of interest. A time along a common chromatographic time is scale determined corresponding to maximum overlay of the ion signals measured for each of the plurality of candidate fragment ions. Finally, the determined time is assigned as the time of elution of the peptide of interest from the liquid chromatography column. In particular, the chromatographic data is acquired during selective reaction monitoring of an eluate from the liquid chromatography column containing the peptide of interest. The chromatographic data includes ion signals measured along the common chromatographic time scale for each of the plurality of candidate fragment ions.

Abstract: A method and apparatus minimize battery discharge of mobile communication devices in short range wireless radio communication networks by switching receiving antennas to minimize transmitted power for a mobile communication device. Multiple receiving antennas and at least one transmitting antenna are used. The receiving antennas are switched for each mobile communication device to minimize transmitted power required by a mobile communication device. Switching between receiving antennas is accomplished by measuring power of a signal received from a mobile communication device at each receiving antenna, and selecting a receiving antenna based on the measured power. A database of switchings is maintained for the mobile communication devices, and an initial selection of a receiving antenna is based on the last switching or a trend indicated by most recent switchings. Alternatively, the initial switching is to a centrally located receiving antenna.

Abstract: A data communication for a handoff mobile unit is maintained by data forwarding through neighboring mobile units in indoor wireless cellular communication networks operates such that, when the master unit has no available channels, the mobile unit switches over to master status to create an ad hoc cell. The mobile unit then pages neighboring slave mobile units for data forwarding assistance. The mobile unit chooses one or more slave mobile units and establishes wireless links with the chosen slave mobile units. These chosen mobile units then have two masters; one the master unit of the cell and the other the handoff mobile unit which has created the ad hoc cell. A list of the slave mobile units in the ad hoc cell is sent to the network server, and data communication proceeds with data forwarding through the chosen mobile slave units. When a channel becomes available with the master unit for the cell, the handoff mobile unit becomes a slave mobile unit to the master unit and the ad hoc cell is dissolved.