Abstract: An apparatus for monitoring a surgical procedure includes a MALDI-TOF mass spectrometer comprising a load lock, an ionization chamber, and an ion detector. A first video camera produces an optical image of an operating field of the surgical procedure. A sample extracting device extracts the tissue sample at the location within the optical image of the operating field. A sample preparation system prepares MALID-TOF samples by depositing an extract of the extracted tissue sample on a sample plate together with a MALDI matrix. A sample plate loading mechanism loads the sample plate into the MALDI-TOF mass spectrometer. A second video camera produces an optical image of the sample plate and records a location of the extracted tissue sample.

Abstract: A MALDI ion source for tandem mass spectrometers includes a pulsed energy source that generates a pulse of ions from a sample on a sample plate. An ion accelerator includes an input that receives the pulse of ions from the pulsed energy source and generates an electric field that accelerates the pulse of ions. An ion decelerator that generates an electric field that is a mirror image of the electric field generated by the ion accelerator that accelerates the pulse of ions so that the ion decelerator decelerates the accelerated pulse of ions and transmits the decelerated pulse of ions through an exit aperture.

Abstract: An apparatus for ligand binding assays includes an incubator that incubates a plurality of beads with a sample of interest wherein each of the plurality of beads comprises a tag of predetermined mass and a bait molecule. A washer washes the incubated beads so that weakly bound molecules are removed while strongly bound molecules are retained. A sample plate loader loads the washed beads into the sample plate such that respective ones of the plurality of beads are loaded into respective ones of the plurality of well. A sprayer deposits matrix assisted laser desorption ionization (MALDI) matrix material on the surface of the sample plate so that each of the plurality of beads is exposed to MALDI matrix material. A MALDI-TOF mass spectrometer receives the sample plate and performs mass spectrometry on samples in the plurality of wells. A computer executes an algorithm that analyzes the mass spectra.

Abstract: An apparatus for molecular imaging of biological samples includes a first optical port configured to receive a first pulsed optical beam that is directed in an optical path along an optical axis. A transparent target that include a first surface having an electrically conductive surface that supports a biological sample under analysis and a second surface is positioned in the optical path along the optical axis. A moveable target mount is configured to translate the transparent target to a plurality of predetermined locations. A first optical focusing element is configured to focus the first pulsed optical beam to a first predetermined diameter at the first surface of the transparent target. A second optical port is configured to receive a second pulsed optical beam that is directed in a second optical path along the optical axis.

Abstract: A MALDI ion source for tandem mass spectrometers includes a pulsed energy source that generates a pulse of ions from a sample on a sample plate. An ion accelerator includes an input that receives the pulse of ions from the pulsed energy source and generates an electric field that accelerates the pulse of ions. An ion decelerator that generates an electric field that is a mirror image of the electric field generated by the ion accelerator that accelerates the pulse of ions so that the ion decelerator decelerates the accelerated pulse of ions and transmits the decelerated pulse of ions through an exit aperture.

Abstract: An apparatus for molecular imaging of biological samples includes a first optical port configured to receive a first pulsed optical beam that is directed in an optical path along an optical axis. A transparent target that include a first surface having an electrically conductive surface that supports a biological sample under analysis and a second surface is positioned in the optical path along the optical axis. A moveable target mount is configured to translate the transparent target to a plurality of predetermined locations. A first optical focusing element is configured to focus the first pulsed optical beam to a first predetermined diameter at the first surface of the transparent target. A second optical port is configured to receive a second pulsed optical beam that is directed in a second optical path along the optical axis.

Abstract: An apparatus for ligand binding of biological samples includes a bead well configured to confine a plurality of magnetic beads. A sample well comprises a filter bottom configured to contain samples of interest. A first magnetic bead picker captures magnetic beads from the bead well and releases the captured magnetic beads into the sample well. An incubator incubates the magnetic beads in the sample well binding the bait molecules to sample molecules contained in the sample of interest. A washer washes the incubated magnetic beads removing weakly bound sample molecules while retaining magnetic beads comprising strongly bound sample molecules. A second magnetic bead picker captures the magnetic beads comprising strongly bound sample molecules from the sample well and releases the captured magnetic beads comprising strongly bound samples onto a sample plate. A matrix material applicator deposits MALDI matrix material onto a surface of the sample plate.

Abstract: A mass spectrometer system for analysis of clinical samples includes a source of clinical samples. A controller receives the clinical samples from the source of clinical samples. A sample preparation system receives clinical sample from the controller and processes the samples to produce an extract suitable for analysis by MALDI-TOF mass spectrometry and deposits the extract on a sample plate together with a MALDI matrix. A sample plate loading mechanism transports sample plates from the sample preparation system into an evacuated ion source of a MALDI-TOF mass spectrometer. A MALDI-TOF mass spectrometer ionizes and analyzes samples on the sample plate and generates a mass spectrum of components in the clinical samples. A computer system receives data from the MALDI-TOF mass spectrometer and processes and interprets the data to generate a mass spectrum.

Abstract: An apparatus for ligand binding assays includes an incubator that incubates a plurality of beads with a sample of interest wherein each of the plurality of beads comprises a tag of predetermined mass and a bait molecule. A washer washes the incubated beads so that weakly bound molecules are removed while strongly bound molecules are retained. A sample plate loader loads the washed beads into the sample plate such that respective ones of the plurality of beads are loaded into respective ones of the plurality of well. A sprayer deposits matrix assisted laser desorption ionization (MALDI) matrix material on the surface of the sample plate so that each of the plurality of beads is exposed to MALDI matrix material. A MALDI-TOF mass spectrometer receives the sample plate and performs mass spectrometry on samples in the plurality of wells. A computer executes an algorithm that analyzes the mass spectra.

Abstract: An apparatus for monitoring a surgical procedure includes a MALDI-TOF mass spectrometer comprising a load lock, an ionization chamber, and an ion detector. A first video camera produces an optical image of an operating field of the surgical procedure. A sample extracting device extracts the tissue sample at the location within the optical image of the operating field. A sample preparation system prepares MALID-TOF samples by depositing an extract of the extracted tissue sample on a sample plate together with a MALDI matrix. A sample plate loading mechanism loads the sample plate into the MALDI-TOF mass spectrometer. A second video camera produces an optical image of the sample plate and records a location of the extracted tissue sample.

Abstract: A method for identifying microorganisms by MALDI-TOF mass spectrometry includes acquiring a MALDI mass spectrum of a microorganism, detecting peaks in the acquired MALDI spectrum, generating a peak list comprising mass and intensity from the detected peaks in the acquired MALDI spectrum, acquiring a database of protein sequences deduced from DNA sequences for microorganisms, generating a sub-database of ribosomal proteins from the protein sequences and their masses in the database, matching masses of the detected peaks in the acquired MALDI spectrum to masses of the ribosomal proteins in the generated sub-database, scoring the matches obtained above for each represented microorganism, generating a peak list of accurate masses of matched ribosomal proteins, recalibrating the peak list comprising mass and intensity with the peak list of accurate masses of matched ribosomal proteins, identifying a microorganism with the highest score, and repeating until a desired improvement in the recalibrated peak list or a v

Abstract: An ion accelerator for a time-of-flight mass spectrometer includes a pulsed ion accelerator positioned proximate to a sample plate and having an electrode that is electrically connected to the sample plate. An accelerator power supply generates an accelerating potential on the ion accelerator electrode that accelerates a pulse of ions generated from the sample positioned on the sample plate. An ion focusing electrode is positioned after the pulsed ion accelerator. A potential applied to the ion focusing electrode focuses the pulse of ions into a substantially parallel beam propagating in an ion flight path. A static ion accelerator is positioned proximate to the ion focusing electrode with an input that receives the pulse of ions focused by the ion focusing electrode. The static ion accelerator accelerating the focused pulse of ions.

Abstract: A method for organism identification using MALDI TOF mass spectrometry includes generating a searchable database. A mass spectrum is acquired from a sample. Peak detection of the acquired mass spectrum is performed, binned, and a vector is generated. Dot products are computed between the generated vector of peak detected mass spectrum and averaged binned spectrum for each isolate. A relative probability that acquired mass spectrum matches a spectrum from each isolate in the searchable database is computed. A logarithmic score for matching the acquired mass spectrum with the mass spectrum is computed from each isolate. The logarithmic score for matching the acquired mass spectrum is compared with the mass spectrum from each isolate to a predetermined minimum passing score. A list of isolates is generated with greater than the predetermined minimum score. The probability rank and logarithmic score are then reported for each isolate with a minimum passing score.

Abstract: A mass spectrometer system for analysis of clinical samples includes a source of clinical samples. A controller receives the clinical samples from the source of clinical samples. A sample preparation system receives clinical sample from the controller and processes the samples to produce an extract suitable for analysis by MALDI-TOF mass spectrometry and deposits the extract on a sample plate together with a MALDI matrix. A sample plate loading mechanism transports sample plates from the sample preparation system into an evacuated ion source of a MALDI-TOF mass spectrometer. A MALDI-TOF mass spectrometer ionizes and analyzes samples on the sample plate and generates a mass spectrum of components in the clinical samples. A computer system receives data from the MALDI-TOF mass spectrometer and processes and interprets the data to generate a mass spectrum.

Abstract: A method for assaying an analyte in a bodily fluid from a subject includes collecting a sample of the bodily fluid comprising an analyte of interest from a subject. A sample with the bodily fluid comprising the analyte of interest suitable for analysis by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF) is then prepared. Mass spectrometry is then performed to determine mass-to-charge ratios and ion abundances of the bodily fluid or its components. The mass-to-charge ratio values and the ion abundance of each of these ratios are then analyzed using calibration standards to interpret a resulting mass spectrum and to provide quantitative information.

Abstract: A sample plate handling system for a time-of-flight mass spectrometer includes a transport chamber and a mass spectrometer chamber that is mechanically coupled to transport chamber. A vacuum chamber is coupled through a bypass valve to the transport chamber. A two-dimensional translation stage is positioned in the mass spectrometer chamber. A sample plate transporter is mounted on the two-dimensional translation stage. A first portion of the sample plate transporter is mechanically attached to the two-dimensional translation stage. A second portion of the sample plate transporter defines a sample plate receiver that is positioned in the transport chamber. A sealing orifice located between the first and the second portions connects the transport chamber and the mass spectrometer chamber.

Abstract: A sample plate handling system for a time-of-flight mass spectrometer includes a transport chamber and a mass spectrometer chamber that is mechanically coupled to transport chamber. A vacuum chamber is coupled through a bypass valve to the transport chamber. A two-dimensional translation stage is positioned in the mass spectrometer chamber. A sample plate transporter is mounted on the two-dimensional translation stage. A first portion of the sample plate transporter is mechanically attached to the two-dimensional translation stage. A second portion of the sample plate transporter defines a sample plate receiver that is positioned in the transport chamber. A sealing orifice located between the first and the second portions connects the transport chamber and the mass spectrometer chamber.

Abstract: A sample plate handling system for a time-of-flight mass spectrometer includes a transport chamber and a mass spectrometer chamber that is mechanically coupled to transport chamber. A two-dimensional translation stage is positioned in the mass spectrometer chamber. A sample plate transporter is mounted on the two-dimensional translation stage. A first portion of the sample plate transporter is mechanically attached to the two-dimensional translation stage. A second portion of the sample plate transporter defines a sample plate receiver that is positioned in the transport chamber. A sealing surface located between the first and the second portions connects the transport chamber and the mass spectrometer chamber.

Abstract: A sample plate handling system for a time-of-flight mass spectrometer includes a sample plate for supporting samples for analysis. A first sample plate receiver is positioned in a first chamber. First and second sample plate receivers are positioned in a second chamber. A first gate valve isolates the first and second chambers when closed and allows transfer of sample plates between the first sample plate receiver in the first chamber and one of the first and second sample plate receivers in the second chamber when the first gate valve is open. A first linear extender pushes a sample plate from the first sample plate receiver in the first chamber to the first sample plate receiver positioned in the second chamber, and then retracts a second sample plate from the second sample plate receiver positioned in the second chamber and transports the second sample plate to the first sample plate receiver in the first chamber. A first sample plate receiver is positioned in a third chamber.

Abstract: An ion accelerator for a time-of-flight mass spectrometer includes a pulsed ion accelerator positioned proximate to a sample plate and having an electrode that is electrically connected to the sample plate. An accelerator power supply generates an accelerating potential on the ion accelerator electrode that accelerates a pulse of ions generated from the sample positioned on the sample plate. An ion focusing electrode is positioned after the pulsed ion accelerator. A potential applied to the ion focusing electrode focuses the pulse of ions into a substantially parallel beam propagating in an ion flight path. A static ion accelerator is positioned proximate to the ion focusing electrode with an input that receives the pulse of ions focused by the ion focusing electrode. The static ion accelerator accelerating the focused pulse of ions.