Abstract: A novel software application method, as integrated with various scientific instruments, is introduced herein that allows new capabilities to be added to the language at runtime without, if desired, having to re-compile the application. As part of the software capabilities, the macro programming language presented herein enables automated connection between inputs and outputs of action statements within a script with visual feedback for configuration verification. As another aspect, the macro programming language of the present invention provides for automation of different spectroscopic applications, which if desired, also allows for the automatic generation of a configurable user interface connected to the intent of the macro.

Abstract: An apparatus is described in which an optical fiber is mounted within a fiber optic holder which includes the non-rotating shaft of a linear actuator. The fiber holder may be held captive in order to restrain the fiber holder and, consequently, the fiber mounted therein, from rotating during operation of the linear actuator, thereby resulting in linear travel with minimal rotational effects and minimal change in optical alignment of the fiber during travel. In addition, an optical path length sensor in conjunction with an optimized absorbance method of operation is utilized herein to provide micron precision of the displacement between respective receiving and transmission fibers so as to enable precise absorbance measurements from about 0.005 up to about 2.0 Absorbance Units for any given path length.

Abstract: A dual-mode method and apparatus of selectively measuring samples in either a vessel or as a surface tension retained sample held between two opposing pedestals is introduced. In either configuration, such modes further contain optical paths from a source system through a small-volume or large-volume sample to a spectrometer based system. Such a system enables a user to measure samples with absorbances ranging from about 0.005 up to about 2.0 Absorbance Units for any given wavelength.

Abstract: The present invention is directed to methods of merging spectral data resulting from collision fragmentation processes, such as, for example, Pulsed Q Dissociation (PQD), high-energy collision-induced dissociation (HCD), electron transfer disassociation (ETD), collision-induced dissociation (CID), and photo-dissociation processes, such as, but not limited to, infrared multi-photon photo-dissociation (IRMPD), to provide the desired qualitative and quantitative information on a single peptide. By merging such ETD, CID, or IRMPD scans with corresponding HCD scans that are obtained on the same precursor, the quality of the resulting spectrum is increased so as to provide more confident identification of peptides and correspondingly the quantification is enhanced because the HCD method of the MS/MS spectrum produces higher abundances of detectable reporter ions. Such methods, as disclosed herein, are especially applicable for peptides which experience predominant neutral loss in the ion trap, e.g., phosphorylated.

Abstract: A Raman optical method and apparatus is utilized to automatically and accurately recognize laser power measurements made at a desired illumination sample plane. From such a configuration, the methods and systems disclosed herein, enable the support of multiple optical wavelengths coupled with essential components, such as, but not limited to, filters, objectives, reflectors, etc., to provide the capability of displaying and controlling the optical power at the desired sample plane through storage of power calibration factors that are associated with such components. In particular, the system utilized herein, can recognize the installation of components and recalls stored calibration factors that are associated with such components to ensure an accurate power measurement at the illuminated sample plane.

Abstract: A multi-resolution mass spectrometer system and intra-scanning method is introduced to enhance the measured peak resolution at different regions of a given mass spectrum while not significantly increasing the total duration of the scan. Such an arrangement enables extra resolution where necessary, such as, for example, when incorporating a slower scan rate only over a predetermined narrow low mass marker region of a given mass spectrum. Once past the marker region, the scan rate can be increased to provide the appropriate resolution for peptide identification.

Abstract: A system for preventing backflow as part of an ion source arrangement is introduced. Such a system incorporates a novel continuous flow guide within a source, such as an API ion source. In the spray direction, the cross-sectional area that defines the first portion of the internal volume initially decreases in a convergent-like manner and thereafter increases in a divergent-like manner towards the exit opening of the source housing. Such a flow guide has been designed as an integral part of an ion source housing to provide for an optimal unidirectional flow past a sampling orifice of a mass spectrometer inlet. Accordingly, the novel design of the present invention prevents recirculation and thus minimizes carryover, chemical noise, and source turbulence and as an added benefit, enables a user to easily clean such a system during maintenance.

Abstract: A mass spectrometer data dependent method and apparatus is introduced to alter scanning parameters based upon data acquired during that scan. Such a method an apparatus may include the identification of ion species of interest meeting user specified criteria so that a determination can be made as to whether or not the present scan is to be continued, terminated, or alternatively paused while such a decision is being made. Such a method of operation saves overall cycle time and allows examination of, for example, marker ion ratios for additional peptides that might otherwise be missed.

Abstract: In an energy dispersive spectrometer wherein event (particle/photon) detection is performed by counting events spaced by greater than a shaping time, events which are spaced by less than the shaping time are also collected and counted. These “combined events” are treated similarly to “single events” which are spaced by greater than the shaping time, and can be used to generate combined-event spectra for comparison and/or use with the conventional single-event spectra. The combined-event spectra can be compared to the single-event spectra to provide an indication of data quality; can be subtracted from the single-event spectra to remove artifacts, and/or can be deconvolved into a single-event spectrum to increase the resolution of the single-event spectrum.

Abstract: A method of analyzing data from a mass spectrometer provides data-dependent acquisition. An extracted ion chromatogram (XIC) is created for each m/z data point of mass spectral scans and the XIC for each m/z data point are correlated to a model function to obtain a XIC correlation value. A weighting function is applied to the XIC correlation value to obtain a current weighted intensity for each m/z point, which is used to reconstruct a weighted mass spectrum. The value or range of intensities of interest of the weighted intensity data or raw data is transformed from the time domain into the frequency domain, and the transformed data is used to make a real-time decision for the data-dependent acquisition. The data-dependent acquisition can be the performance of tandem mass spectrometry. A sample processing apparatus receives the sample and a computer readable medium provides instructions to the apparatus.

Abstract: An automatic gain control (AGC) technique and apparatus is introduced herein for any temporally non-uniform ion beam, such as, for example, an ion beam produced by a MALDI ion source so as to minimize space charge effects. The disclosed configurations and techniques can be achieved by using an ion optical gating element and applying a desired signal waveform (e.g., a square wave) having a predetermined duty cycle. The applied voltage amplitude of such a signal can be configured to switch between a voltage which fully transmits the ions, and a voltage which does not transmit any ions. The frequency is chosen to result in a period which is significantly lower than the smallest non-uniformity period. Techniques of the present invention can also be extended to methods of AGC which can use a single ion injection event from the ion source to avoid variations in ion numbers from an unstable ion source.

Abstract: A method and apparatus of combining two independent multipoles in an interlaced fashion to form a resultant multipole structure is introduced. Such an arrangement enables ions from two separate sources to be merged along a predetermined longitudinal direction but also enables in the reverse path, predetermined portions of ions from a single source to be directed along one or more ion channel paths to also enable, for example, simultaneous collection by a Time of Flight (TOF) mass analyzer and an ion trap.

Abstract: A device for improved transportation and focusing of ions in a low vacuum or atmospheric-pressure region of a mass spectrometer is constructed from one or more electro-dynamic or electrostatic focusing lenses that is/are coupled to the first electrode of a stacked ring ion guide (SRIG) to which oscillatory (e.g., radio-frequency) voltages are applied. Such configurations as disclosed herein, minimizes deleterious field effects and/or repositioning problems of desired ion transfer instruments that utilize such stacked ring ion guides by generally configuring the outlet end of the ion transfer device to a desired position within the electro-dynamic or electro-static focusing lens(es).

Abstract: A method and apparatus of combining an ion volume, a lens stack, and an ion optic that similarly cooperates with a detached multipole ion guide is herein incorporated into a single sub-assembly that can be removed from a mass spectrometer instrument without venting. Such an arrangement allows an operator to clean all parts of the ion path that get contaminated in normal operation, reassemble and reinsert in a timely manner and then pump down to an acceptable vacuum without having to vent the system.

Abstract: Auxiliary electrodes for creating drag fields may be provided as arrays of finger electrodes on thin substrates such as printed circuit board material for insertion between main RF electrodes of a multipole. A progressive range of voltages can be applied along lengths of the auxiliary electrodes by implementing a voltage divider that utilizes static resisters interconnecting individual finger electrodes of the arrays. Dynamic voltage variations may be applied to individual finger electrodes or to groups of the finger electrodes.

Abstract: An optical method and apparatus is utilized to provide rapid spatial averaging over a large sample area in a Raman spectrometer, without defocusing of the optical source or the collection optics. Spatial averaging provides a representative spectrum of a sample that is inhomogeneous, either in its composition or surface characteristics. The spatial averaging configurations and methods disclosed herein also reduce sample degradation or burning resulting from the high intensity of the directed optical source. Moreover, the dimensions of the sample area of the spatial averaging methods and configurations of the present invention are adjusted to match specific sampling requirements.

Abstract: The present invention utilizes novel laser-based, high-brightness, high-spatial-resolution, pencil-beam sources of spectrally pure hard x-ray and gamma-ray radiation to induce resonant scattering in specific nuclei, i.e., nuclear resonance fluorescence. By monitoring such fluorescence as a function of beam position, it is possible to image in either two dimensions or three dimensions, the position and concentration of individual isotopes in a specific material configuration. Such methods of the present invention material identification, spatial resolution of material location and ability to locate and identify materials shielded by other materials, such as, for example, behind a lead wall. The foundation of the present invention is the generation of quasimonochromatic high-energy x-ray (100's of keV) and gamma-ray (greater than about 1 MeV) radiation via the collision of intense laser pulses from relativistic electrons. Such a process as utilized herein, i.e.

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: A novel UWB communications method and system that provides self-organization for wireless sensor networks is introduced. The self-organization is in terms of scalability, power conservation, channel estimation, and node synchronization in wireless sensor networks. The UWB receiver in the present invention adds two new tasks to conventional TR receivers. The two additional units are SNR enhancing unit and timing acquisition and tracking unit.

Abstract: A method of processing a composite material to tailor white light emission of the resulting composite during excitation. The composite material is irradiated with a predetermined power and for a predetermined time period to reduce the size of a plurality of nanocrystals and the number of a plurality of traps in the composite material. By this irradiation process, blue light contribution from the nanocrystals to the white light emission is intensified and red and green light contributions from the traps are decreased.