Abstract: Described herein are mass spectrometry systems and methods which improve the accuracy of isobaric tag-based quantification by alleviating the pervasive problem of precursor interference and co-isolation of impurities through gas-phase purification. During the gas-phase purification, the mass-to-charge ratios of precursor ions within at least a selected range are selectively changed allowing ions having similar unmodified mass-to-charge ratios to be separated before further isolation, fragmentation or analysis.

Abstract: Described herein are mass spectrometry systems and methods which improve the accuracy of isobaric tag-based quantification by alleviating the pervasive problem of precursor interference and co-isolation of impurities through gas-phase purification. During the gas-phase purification, the mass-to-charge ratios of precursor ions within at least a selected range are selectively changed allowing ions having similar unmodified mass-to-charge ratios to be separated before further isolation, fragmentation or analysis.

Abstract: Enzymes for producing non-straight-chain fatty acids, microorganisms comprising the enzymes, and in vivo and in vitro uses of the enzymes. Provided are enzymes capable of producing various non-straight-chain fatty acids, including branched-chain fatty acids, cyclic fatty acids, and furan-containing fatty acids. The enzymes include RSP2144, RSP1091, and RSP1090 from Rhodobacter sphaeroides and homologs thereof. The enzymes can be purified to produce non-straight-chain fatty acids in vitro or expressed in microorganisms to produce non-straight-chain fatty acids in vivo. The microorganisms can be fine-tuned to produce a specific type of non-straight-chain fatty acid by expressing, overexpressing, or deleting the enzymes in various combinations.

Abstract: The invention provides methods, systems and algorithms for identifying high-resolution mass spectra. In some embodiments, an analyte is ionized and analyzed using high-resolution mass spectrometry (MS) at high mass accuracy (such as ?75 ppm or ?30 ppm) and the obtained mass spectra are matched with one or more prospective candidate molecules or chemical formulas. The invention provide, for example, methods and systems wherein the possible fragments that can be generated from the candidate molecules or chemical formulas are determined as well as the masses of each of these fragments. The invention provide, for example, methods and systems wherein the high-resolution mass spectra are then compared with the calculated fragment masses for each of the candidate molecules or chemical formula, and the portion of the high-resolution mass spectra that corresponds or can be explained by the calculated fragment masses is determined.

Abstract: Described herein are mass spectrometry systems and methods which improve the accuracy of isobaric tag-based quantification by alleviating the pervasive problem of precursor interference and co-isolation of impurities through gas-phase purification. During the gas-phase purification, the mass-to-charge ratios of precursor ions within at least a selected range are selectively changed allowing ions having similar unmodified mass-to-charge ratios to be separated before further isolation, fragmentation or analysis.

Abstract: Described herein are mass spectrometry systems and methods which improve the accuracy of isobaric tag-based quantification by alleviating the pervasive problem of precursor interference and co-isolation of impurities through gas-phase purification. During the gas-phase purification, the mass-to-charge ratios of precursor ions within at least a selected range are selectively changed allowing ions having similar unmodified mass-to-charge ratios to be separated before further isolation, fragmentation or analysis.

Abstract: Enzymes for producing non-straight-chain fatty acids, microorganisms comprising the enzymes, and in vivo and in vitro uses of the enzymes. Provided are enzymes capable of producing various non-straight-chain fatty acids, including branched-chain fatty acids, cyclic fatty acids, and furan-containing fatty acids. The enzymes include RSP2144, RSP1091, and RSP1090 from Rhodobacter sphaeroides and homologs thereof. The enzymes can be purified to produce non-straight-chain fatty acids in vitro or expressed in microorganisms to produce non-straight-chain fatty acids in vivo. The microorganisms can be fine-tuned to produce a specific type of non-straight-chain fatty acid by expressing, overexpressing, or deleting the enzymes in various combinations.

Abstract: The invention provides methods, systems and algorithms for identifying high-resolution mass spectra. In some embodiments, an analyte is ionized and analyzed using high-resolution mass spectrometry (MS) at high mass accuracy (such as ?75 ppm or ?30 ppm) and the obtained mass spectra are matched with one or more prospective candidate molecules or chemical formulas. The invention provide, for example, methods and systems wherein the possible fragments that can be generated from the candidate molecules or chemical formulas are determined as well as the masses of each of these fragments. The invention provide, for example, methods and systems wherein the high-resolution mass spectra are then compared with the calculated fragment masses for each of the candidate molecules or chemical formula, and the portion of the high-resolution mass spectra that corresponds or can be explained by the calculated fragment masses is determined.

Abstract: Described herein are mass spectrometry systems and methods which utilize a dynamic a new data acquisition/instrument control methodology. These systems and methods employ novel artificial intelligence algorithms to greatly increase quantitative and/or identification accuracy during data acquisition. In an embodiment, the algorithms can adapt the instrument methods and systems during data acquisition to direct data acquisition resources to increase quantitative or identification accuracy of target analytes, such as proteins, peptides, and peptide fragments.

Abstract: A fast and sensitive method and device for protein sequencing are disclosed. The method uses a combination of Edman degradation chemistry and mass spectrometry to sequence proteins and polypeptides. A peptide degradation reaction is performed on a polypeptide or protein ion reactant in the gas phase. The reaction yields a first ion product corresponding to a first amino acid residue of the polypeptide or protein reactant and a polypeptide or protein fragment ion. The mass-to-charge ratio for the first ion product, or the polypeptide or protein fragment ion, or both, is then determined. The first amino acid residue of the polypeptide or protein reactant is then identified from the mass-to-charge ratio so determined.

Abstract: Described herein are mass spectrometry systems and methods which improve the accuracy of isobaric tag-based quantification by alleviating the pervasive problem of precursor interference and co-isolation of impurities through gas-phase purification. During the gas-phase purification, the mass-to-charge ratios of precursor ions within at least a selected range are selectively changed allowing ions having similar unmodified mass-to-charge ratios to be separated before further isolation, fragmentation or analysis.

Abstract: Described herein are mass spectrometry systems and methods which utilize a dynamic a new data acquisition/instrument control methodology. These systems and methods employ novel artificial intelligence algorithms to greatly increase quantitative and/or identification accuracy during data acquisition. In an embodiment, the algorithms can adapt the instrument methods and systems during data acquisition to direct data acquisition resources to increase quantitative or identification accuracy of target analytes, such as proteins, peptides, and peptide fragments.

Abstract: The present invention provides systems, devices, device components and structures for modulating the intensity and/or energies of electrons, including a beam of incident electrons. In some embodiments, for example, the present invention provides nano-structured semiconductor membrane structures capable of generating secondary electron emission. Nano-structured semiconductor membranes of this aspect of the present invention include membranes having an array of nanopillar structures capable of providing electron emission for amplification, filtering and/or detection of incident radiation, for example secondary electron emission and/or field emission. Nano-structured semiconductor membranes of the present invention are useful as converters wherein interaction of incident primary electrons and nanopillars of the nanopillar array generates secondary emission.

Abstract: The present invention provides systems, devices, device components and structures for modulating the intensity and/or energies of electrons, including a beam of incident electrons. In some embodiments, for example, the present invention provides nano-structured semiconductor membrane structures capable of generating secondary electron emission. Nano-structured semiconductor membranes of this aspect of the present invention include membranes having an array of nanopillar structures capable of providing electron emission for amplification, filtering and/or detection of incident radiation, for example secondary electron emission and/or field emission. Nano-structured semiconductor membranes of the present invention are useful as converters wherein interaction of incident primary electrons and nanopillars of the nanopillar array generates secondary emission.

Abstract: This invention provides methods, devices and device components for preparing ions from liquid samples containing chemical species and methods and devices for analyzing chemical species in liquid samples. The present invention provides an ion source for generating analyte ions having a selected charge state distribution, such as a reduced charged state distribution, that may be effectively interfaced with a variety of charged particle analyzers, including virtually any type of mass spectrometer.

Abstract: A fast and sensitive method and device for protein sequencing are disclosed. The method uses a combination of Edman degradation chemistry and mass spectrometry to sequence proteins and polypeptides. A peptide degradation reaction is performed on a polypeptide or protein ion reactant in the gas phase. The reaction yields a first ion product corresponding to a first amino acid residue of the polypeptide or protein reactant and a polypeptide or protein fragment ion. The mass-to-charge ratio for the first ion product, or the polypeptide or protein fragment ion, or both, is then determined. The first amino acid residue of the polypeptide or protein reactant is then identified from the mass-to-charge ratio so determined.

Abstract: The invention provides devices, device configurations and methods for improved sensitivity, resolution and efficiency in mass spectrometry, particularly as applied to biological molecules, including biological polymers, such as proteins and nucleic acids. More particularly, the invention provides methods and devices for analyzing and detecting electrically charged particles, especially suitable for gas phase ions generated from high molecular weight compounds. In one aspect, the invention provides devices and methods for determining the velocity, charged state or both of electrically charged particles and packets of electrically charged particles. In another aspect, the invention provides methods and devices for the time-of-flight analysis of electrically charged particles comprising spatially collimated sources. In another aspect, the invention relates to multiple detection using inductive detectors, improved methods of signal averaging and charged particle detection in coincidence.

Abstract: The invention provides devices, device configurations and methods for improved sensitivity, resolution and efficiency in mass spectrometry, particularly as applied to biological molecules, including biological polymers, such as proteins and nucleic acids. More particularly, the invention provides methods and devices for analyzing and detecting electrically charged particles, especially suitable for gas phase ions generated from high molecular weight compounds. In one aspect, the invention provides devices and methods for determining the velocity, charged state or both of electrically charged particles and packets of electrically charged particles. In another aspect, the invention provides methods and devices for the time-of-flight analysis of electrically charged particles comprising spatially collimated sources. In another aspect, the invention relates to multiple detection using inductive detectors, improved methods of signal averaging and charged particle detection in coincidence.

Abstract: The charge state of ions produced by electrospray ionization is reduced in a controlled manner to yield predominantly singly charged ions through reactions with bipolar ions generated using a 210Po alpha particle source or equivalent. The multiply charged ions generated by the electrospray undergo charge reduction in a charge reduction chamber. The charge-reduced ions are then detected using a commercial orthogonal electrospray TOF mass spectrometer, although the charge reduction chamber can be adapted to virtually any mass analyzer. The results obtained exhibit a signal intensity drop-off with increased oligonucleotide size similar to that observed with MALDI mass spectrometry, yet with the softness of ESI and without the off-line sample purification and pre-separation required by MALDI.

Abstract: Methods and devices for use in mass spectral analysis of samples. In particular, methods and devices for generating ions from liquid samples containing chemical species with high molecular masses. These methods and devices provide a continuous or pulsed stream of gas phase analyte ions of either positive polarity, negative polarity or both possessing either a selected fixed charge-state distribution or one that may be selectively varied with time. More specifically, ion sources with adjustable control of the charge-state distribution of the gas phase analyte ions generated are provided in which charged droplets and/or gas phase analyte ions are exposed to electrons and/or gas phase reagent ions generated by a reagent ion source to provide desired control. A corona discharge exemplifies the reagent ion source employed in charge-state distribution control.