Abstract: In an ion mobility-mass spectrometry (IM-MS) system, an ion mass-isolated data set is acquired by operating a mass filter to apply a mass isolation window having an m/z width such that the mass isolation window moves through a sequence of window positions, each window position being defined by an IM drift time value and an m/z ratio value. The m/z width of the mass isolation window and the sequence of window positions are determined such that the mass isolation window captures ions in a region of interest of a larger all-ions data set. The isolation window may be a wideband isolation window. In comparison to the all-ions data set, the mass-isolated data set may yield reduced ion signal interference and increased selectivity for analytes of interest.

Abstract: In an ion mobility-mass spectrometry (IM-MS) system, an ion mass-isolated data set is acquired by operating a mass filter to apply a mass isolation window having an m/z width such that the mass isolation window moves through a sequence of window positions, each window position being defined by an IM drift time value and an m/z ratio value. The m/z width of the mass isolation window and the sequence of window positions are determined such that the mass isolation window captures ions in a region of interest of a larger all-ions data set. The isolation window may be a wideband isolation window. In comparison to the all-ions data set, the mass-isolated data set may yield reduced ion signal interference and increased selectivity for analytes of interest.

Abstract: A method and apparatus for performing time of flight mass spectrometry wherein the number of sums of transients taken for generating a given spectra is determined as a function of a characteristic of the incoming data for that spectrum. For instance, the number of transient measurements taken for a given spectrum output can be determined as a function of the abundance of ions in the sample or the abundance of ions corresponding to a base peak or another selected peak. In yet another embodiment, the collection of transients is terminated when a threshold signal to noise ratio is attained.

Abstract: A method of MALDI sample plate processing includes capturing an image of a plate positioned outside a mass spectrometer. The image is processed to identify one or more attributes of an individual sample on the plate, where the attributes are selected from a position attribute, a geometry attribute and an internal density distribution attribute. A laser impact position is selected within the mass spectrometer based upon one or more of the attributes.

Abstract: A mass spectrometry system is described. The mass spectrometry system comprises: (a) a mass spectrometer; and (b) a controller connected to the mass spectrometer. The controller is configured to: (i) direct the mass spectrometer to acquire a precursor ion spectrum of a sample stream; (ii) analyze, in real-time, the precursor ion spectrum to determine whether a first evaluation criterion is satisfied; (iii) if the first evaluation criterion is satisfied, direct the mass spectrometer to acquire a product ion spectrum of the sample stream; (iv) analyze, in real-time, the product ion spectrum to determine whether a second evaluation criterion is satisfied; and (v) if the second evaluation criterion is satisfied, analyze the product ion spectrum to assign an identification to the product ion spectrum. For certain implementations, the controller allows automated, data-dependent acquisition of mass spectrometry data to improve the efficiency at which peptidic data of interest can be acquired.

Abstract: The invention provides an apparatus for producing an image of a global surface of an ion source sample plate that is exterior to an ion source. In general terms, the apparatus contains a sample plate for an ion source, an imaging device (e.g., a CCD or CMOS camera) and an illumination device that is configured to produce a light beam that contacts the sample plate surface to define a grazing angle between the light beam and the sample plate surface. The apparatus may be present at a location that is remote to the ion source.

Abstract: A method and apparatus for performing time of flight mass spectrometry wherein the number of sums of transients taken for generating a given spectra is determined as a function of a characteristic of the incoming data for that spectrum. For instance, the number of transient measurements taken for a given spectrum output can be determined as a function of the abundance of ions in the sample or the abundance of ions corresponding to a base peak or another selected peak. In yet another embodiment, the collection of transients is terminated when a threshold signal to noise ratio is attained.

Abstract: The invention provides a mass spectrometry system ion source containing a sample plate and an illumination device that is configured to produce a light beam that contacts the sample plate surface to define a grazing angle between the light beam and the sample plate surface. The ion source may also contain an imaging device, e.g., a CCD or CMOS camera or the like, for viewing the area. In one embodiment, the imaging device may be connected to a display, e.g., a video monitor. Methods and mass spectrometry systems empliying the ion source are also provided.

Abstract: An automated method of evaluating an electrospray jet includes: capturing image information about the electrospray jet, enhancing the image information to provide a clearer image when needed, comparing the captured image information, and generating a signal to indicative of the electrospray jet operation. The signal may be used to automatically adjust the electrospray.

Abstract: Methods for specifying the layout of a MALDI sample plate are provided. In general, the methods involve creating a file containing sample plate layout parameters that describe the layout of a MALDI sample plate, and storing the file on a computer readable medium prior to placement of the MALDI sample plate into a MALDI ion source. In many embodiments, the file includes information about the size or shape of the sample plate, or information about the size, shape or position of a sample on the sample plate. In many embodiments, a MALDI sample plate is placed in a MALDI ion source and a stored layout file for the sample plate is accessed and used to position an area of the sample plate in a laser beam. The subject methods, kits and apparatus find use in a variety of different mass spectrometry applications.

Abstract: A method of MALDI sample plate processing includes capturing an image of a plate positioned outside a mass spectrometer. The image is processed to identify one or more attributes of an individual sample on the plate, where the attributes are selected from a position attribute, a geometry attribute and an internal density distribution attribute. A laser impact position is selected within the mass spectrometer based upon one or more of the attributes.

Abstract: A method of MALDI sample plate processing includes capturing an image of a plate positioned outside a mass spectrometer. The image is processed to identify one or more attributes of an individual sample on the plate, where the attributes are selected from a position attribute, a geometry attribute and an internal density distribution attribute. A laser impact position is selected within the mass spectrometer based upon one or more of the attributes.

Abstract: Methods for specifying the layout of a MALDI sample plate are provided. In general, the methods involve creating a file containing sample plate layout parameters that describe the layout of a MALDI sample plate, and storing the file on a computer readable medium prior to placement of the MALDI sample plate into a MALDI ion source. In many embodiments, the file includes information about the size or shape of the sample plate, or information about the size, shape or position of a sample on the sample plate. In many embodiments, a MALDI sample plate is placed in a MALDI ion source and a stored layout file for the sample plate is accessed and used to position an area of the sample plate in a laser beam. The subject methods, kits and apparatus find use in a variety of different mass spectrometry applications.

Abstract: Methods for specifying the layout of a MALDI sample plate are provided. In general, the methods involve creating a file containing sample plate layout parameters that describe the layout of a MALDI sample plate, and storing the file on a computer readable medium prior to placement of the MALDI sample plate into a MALDI ion source. In many embodiments, the file includes information about the size or shape of the sample plate, or information about the size, shape or position of a sample on the sample plate. In many embodiments, a MALDI sample plate is placed in a MALDI ion source and a stored layout file for the sample plate is accessed and used to position an area of the sample plate in a laser beam. The subject methods, kits and apparatus find use in a variety of different mass spectrometry applications.

Abstract: A secure file verification station receives and stores a data file received from a trusted source. The verification station applies a hashing function to the data file, and then encrypts the hash using a unique symmetric encryption key derived from a seed value that is maintained securely within the verification station. The encrypted hash is then appended to the data file. The station is networked to client workstations to which it delivers data files. To verify the integrity of a data file it has received from the verification station, a client workstation sends back the data file to the station, where the encrypted hash is decrypted using the unique symmetric key that is again generated from the seed value. A recomputed hash of the data is compared to the decrypted hash value. If the two hash values are equal, the integrity of the data is verified; otherwise the file has been modified in some way.

Abstract: A mass spectrometer system analyzes a sample with the aid an associated computer system or processor which utilizes a relatively small compound deconvolution data library. The deconvolution library has a specific predefined order. The specific order of the compounds in the library is established based on predetermined knowledge of the sample being tested by the mass spectrometer. A deconvolution technique utilized by the computer system automates a deconvolution technique that would be utilized by an experienced process chemist for a similar sample and associated fragmentation or cracking pattern. The deconvolution technique steps through the deconvolution library's order of compounds and compares each compound's stored spectral data with the sample's spectrum. If it is determined that a compound's spectrum is found in the sample's spectrum, then at least one complete peak associated with the found compound's spectrum is removed from the sample's spectrum.

Abstract: A mass spectrometer system analyzes a sample with the aid an associated computer system or processor which utilizes a relatively small compound deconvolution data library. The deconvolution library has a specific predefined order. The specific order of the compounds in the library is established based on predetermined knowledge of the sample being tested by the mass spectrometer. A deconvolution technique utilized by the computer system automates a deconvolution technique that would be utilized by an experienced process chemist for a similar sample and associated fragmentation or cracking pattern. The deconvolution technique steps through the deconvolution library's order of compounds and compares each compound's stored spectral data with the sample's spectrum. If it is determined that a compound's spectrum is found in the sample's spectrum, then at least one complete peak associated with the found compound's spectrum is removed from the sample's spectrum.

Abstract: A mass spectrometer system analyzes a sample with the aid an associated computer system or processor which utilizes a relatively small compound deconvolution data library. The deconvolution library has a specific predefined order. The specific order of the compounds in the library is established based on predetermined knowledge of the sample being tested by the mass spectrometer. A deconvolution technique utilized by the computer system automates a deconvolution technique that would be utilized by an experienced process chemist for a similar sample and associated fragmentation or cracking pattern. The deconvolution technique steps through the deconvolution library's order of compounds and compares each compound's stored spectral data with the sample's spectrum. If it is determined that a compound's spectrum is found in the sample's spectrum, then at least one complete peak associated with the found compound's spectrum is removed from the sample's spectrum.

Abstract: A mass spectrometer system analyzes a sample with the aid an associated computer system or processor which utilizes a relatively small compound deconvolution data library. The deconvolution library has a specific predefined order. The specific order of the compounds in the library is established based on predetermined knowledge of the sample being tested by the mass spectrometer. A deconvolution technique utilized by the computer system automates a deconvolution technique that would be utilized by an experienced process chemist for a similar sample and associated fragmentation or cracking pattern. The deconvolution technique steps through the deconvolution library's order of compounds and compares each compound's stored spectral data with the sample's spectrum. If it is determined that a compound's spectrum is found in the sample's spectrum, then at least one complete peak associated with the found compound's spectrum is removed from the sample's spectrum.