Abstract: In one aspect of the present invention, the less “useful” spectral data is disregarded from the spectral data resulting from the fragmentation by ETD and candidate charge states for the “useful” data assigned. Knowledge of the first order ion product charge state reduces the subset of comparison data hence aiding in the eventual identification of the precursor ion, and thus aiding in peptide sequence database searching capabilities. Such capabilities include, but are not limited to, computational requirements for database search and data storage, CPU time, the volume taken up on the hard disk to store results, visualization and dissemination of data, and overall improvement in the confidence in the precursor identification. Thus determination of the peptide sequence can be resolved in less time, costing less money, and requiring less computer power.

Abstract: In one aspect of the present invention, the less “useful” spectral data is disregarded from the spectral data resulting from the fragmentation by ETD and candidate charge states for the “useful” data assigned. Knowledge of the first order ion product charge state reduces the subset of comparison data hence aiding in the eventual identification of the precursor ion, and thus aiding in peptide sequence database searching capabilities. Such capabilities include, but are not limited to, computational requirements for database search and data storage, CPU time, the volume taken up on the hard disk to store results, visualization and dissemination of data, and overall improvement in the confidence in the precursor identification. Thus determination of the peptide sequence can be resolved in less time, costing less money, and requiring less computer power.

Abstract: In one aspect of the present invention a new database search methodology is provided that provides a probability that spectral data from a non-ergodic reaction via mass spectrometry matches a candidate sequence from a set of sequences in a database by random. The methodology comprises two parts. The first part pre-processes the spectral data and retains only the most relevant data for the database search. The second part comprises searching a database using the pre-processed spectrum to assign a probability or expectation that the spectrum matches a candidate sequence from a set of sequences in a database by random. The search methodology uses a new probability model, a compound distribution based on the number of product ion mass-to-charge ratios and the number of intensity values that are shared between the product ion spectral data and the sequence database, to accurately predict the probability of the peptide identification being a correct match, and not a random event.

Abstract: In one aspect of the present invention a new database search methodology is provided that provides a probability that spectral data from a non-ergodic reaction via mass spectrometry matches a candidate sequence from a set of sequences in a database by random. The methodology comprises two parts. The first part pre-processes the spectral data and retains only the most relevant data for the database search. The second part comprises searching a database using the pre-processed spectrum to assign a probability or expectation that the spectrum matches a candidate sequence from a set of sequences in a database by random. The search methodology uses a new probability model, a compound distribution based on the number of product ion mass-to-charge ratios and the number of intensity values that are shared between the product ion spectral data and the sequence database, to accurately predict the probability of the peptide identification being a correct match, and not a random event.

Abstract: Methods and apparatus for data-dependent mass spectrometric MS/MS or MSn analysis are disclosed. The methods may include determination of the charge state of an ion species of interest, followed by automated selection of a dissociation type (e.g., CAD, ETD, or ETD followed by a non-dissociative charge reduction or collisional activation) based at least partially on the determined charge state. The ion species of interest is then dissociated in accordance with the selected dissociation type, and an MS/MS or MSn spectrum of the resultant product ions may be acquired.

Abstract: Disclosed is apparatus and method for controlled surface plasmon resonance analysis having a surface plasmon resonance sensor (200) with a derivatized surface plasmon layer (116) in optical communication with the sensor, derivatizing the surface plasmon layer and placing an analyte detection chamber (102) in fluid communication with the derivatized surface plasmon layer. The chamber is adapted (118, 120) for the generation of a molecular interaction bias across the chamber. A conjugate is provided between an analyte and a bias responsive element, wherein the analyte is reactive with the derivatized surface plasmon layer and the bias responsive element changes the response of the analyte to the molecular interaction bias. A conjugated analyte may be introduced into the chamber, generating a molecular interaction.

Abstract: Disclosed is apparatus and method for controlled surface plasmon resonance analysis having a surface plasmon resonance sensor (200) with a derivatized surface plasmon layer (116) in optical communication with the sensor, derivatizing the surface plasmon layer and placing an analyte detection chamber (102) in fluid communication with the derivatized surface plasmon layer. The chamber is adapted (118, 120) for the generation of a molecular interaction bias across the chamber. A conjugate is provided between an analyte and a bias responsive element, wherein the analyte is reactive with the derivatized surface plasmon layer and the bias responsive element changes the response of the analyte to the molecular interaction bias. A conjugated analyte may be introduced into the chamber, generating a molecular interaction.

Abstract: Disclosed is apparatus and method for controlled surface plasmon resonance analysis having a surface plasmon resonance sensor (200) with a derivatized surface plasmon layer (116) in optical communication with the sensor, derivatizing the surface plasmon layer and placing an analyte detection chamber (102) in fluid communication with the derivatized surface plasmon layer. The chamber is adapted (118, 120) for the generation of a molecular interaction bias across the chamber. A conjugate is provided between an analyte and a bias responsive element, wherein the analyte is reactive with the derivatized surface plasmon layer and the bias responsive element changes the response of the analyte to the molecular interaction bias. A conjugated analyte may be introduced into the chamber, generating a molecular interaction.

Abstract: Disclosed is apparatus and method for controlled surface plasmon resonance analysis having a surface plasmon resonance sensor (200) with a derivatized surface plasmon layer (116) in optical communication with the sensor, derivatizing the surface plasmon layer and placing an analyte detection chamber (102) in fluid communication with the derivatized surface plasmon layer. The chamber is adapted (118, 120) for the generation of a molecular interaction bias across the chamber. A conjugate is provided between an analyte and a bias responsive element, wherein the analyte is reactive with the derivatized surface plasmon layer and the bias responsive element changes the response of the analyte to the molecular interaction bias. A conjugated analyte may be introduced into the chamber, generating a molecular interaction.

Abstract: Methods for performing rapid and accurate thermocycling on a sample are disclosed. Use of non-contact heating and cooling sources allows precise temperature control with sharp transitions from one temperature to another to be achieved. A wide range of temperatures can be accomplished according to these methods. In addition, thermocycling can be performed without substantial temperature gradients occurring in the sample. Apparatus for achieving these methods are also disclosed. A method for pumping a sample through microchannels on a microchip using a non-contact heat source is also disclosed.

Abstract: Methods for performing rapid and accurate thermocycling on a sample are disclosed. Use of non-contact heating and cooling sources allows precise temperature control with sharp transitions from one temperature to another to be achieved. A wide range of temperatures can be accomplished according to these methods. In addition, thermocycling can be performed without substantial temperature gradients occurring in the sample. Apparatus for achieving these methods are also disclosed. A method for pumping a sample through microchannels on a microchip using a non-contact heat source is also disclosed.

Abstract: The present invention provides an excitation source which may be used, for example, in conjunction with the scanning of multi-channel electrophoresis chips or capillary arrays. The excitation source is comprised of a source of light, such as a laser beam. A beam expander, an acousto-optic deflector, and a filter are optically aligned with the source of light. A driver is connected to the acousto-optic deflector for controlling the angle of deflection. A system is disclosed which includes the excitation source, a detector for detecting fluorescence from a target chip, and a beam splitter or other device for optically connecting the excitation source to the chip and for optically connecting the chip to the detector. The excitation source may be based on an acousto-optic deflector, an electrooptic deflector, a piezoelectric deflector, or any other electronically controlled device.

Abstract: Methods for performing rapid and accurate thermocycling on a sample are disclosed. Use of non-contact heating and cooling sources allows precise temperature control with sharp transitions from one temperature to another to be achieved. A wide range of temperatures can be accomplished according to these methods. In addition, thermocycling can be performed without substantial temperature gradients occurring in the sample. Apparatus for achieving these methods are also disclosed. A method for pumping a sample through microchannels on a microchip using a non-contact heat source is also disclosed.