Abstract: A method for analyzing samples utilizing stable label isotope tracing includes receiving mass spectrometry (MS) data generated by an MS system performing untargeted data acquisition on a plurality of samples, performing untargeted feature extraction on the unlabeled compound data to generate a data set of first extracted features, generating a plurality of empirical molecular formulas respectively corresponding to the first extracted features, performing targeted isotopologue extraction on the labeled compound data to generate a data set of second extracted features, wherein the targeted isotopologue extraction is based on the empirical molecular formula and retention time of each first extracted feature, and identifying one or more groups of isotopologues from the second extracted features.

Abstract: Reagents and methods for extracting and stabilizing metabolites at room temperature and methods in which metabolites and one or more of proteins, lipids and nucleic acids are extracted from a single sample in a unified workflow.

Abstract: Reagents and methods for extracting and stabilizing metabolites at room temperature and methods in which metabolites and one or more of proteins, lipids and nucleic acids are extracted from a single sample in a unified workflow.

Abstract: A method for analyzing samples utilizing stable label isotope tracing includes receiving mass spectrometry (MS) data generated by an MS system performing untargeted data acquisition on a plurality of samples, performing untargeted feature extraction on the unlabeled compound data to generate a data set of first extracted features, generating a plurality of empirical molecular formulas respectively corresponding to the first extracted features, performing targeted isotopologue extraction on the labeled compound data to generate a data set of second extracted features, wherein the targeted isotopologue extraction is based on the empirical molecular formula and retention time of each first extracted feature, and identifying one or more groups of isotopologues from the second extracted features.

Abstract: Provided herein, among other things, is a method of ionizing a first stream of liquid by an electrospray ion source having a nebulizer, wherein the first stream of liquid may comprise an analyte. In some embodiments, the method may comprise: a) providing the first stream of liquid to the nebulizer; b) adding a second stream of liquid to the first stream of liquid, wherein the second stream of liquid comprises a co-solvent that has a relatively high boiling point and an enhancement solvent that a relatively high boiling; and c) nebulizing and ionizing the resulting liquid.

Abstract: Provided herein, among other things, is a method of ionizing a first stream of liquid by an electrospray ion source having a nebulizer, wherein the first stream of liquid may comprise an analyte. In some embodiments, the method may comprise: a) providing the first stream of liquid to the nebulizer; b) adding a second stream of liquid to the first stream of liquid, wherein the second stream of liquid comprises a co-solvent that has a relatively high boiling point and an enhancement solvent that a relatively high boiling; and c) nebulizing and ionizing the resulting liquid.

Abstract: A method of identifying a biopolymer in a sample that includes one or more biopolymers. The biopolymers may be polypeptides, polynucleotides, or polysaccharides. The method makes use of mass spectral datasets. A first dataset includes measured masses of the one or more biopolymers that are in the sample. A second dataset includes measured masses of a collection of fragments of the one or more biopolymers. The method selects a mass from the first dataset and then matches masses from the second dataset with the selected mass. The matched masses represent fragments of the biopolymer with the selected mass. Once the masses in the second dataset have been matched they are compared to determine a monomer sequence for the biopolymer with the selected mass. The method may be repeated with additional masses in the first dataset.

Abstract: A mass spectrometer having a matrix-assisted laser desorption ionization (MALDI) source which operates at ambient pressure is disclosed.

Abstract: Systems and method for curation of mass spectral libraries. In general, the systems and methods provided herein (a) obtain an experimentally derived mass spectrum of a compound of interest; (b) identify a peak in the mass spectrum that represent an experimental m/z value for an ion fragment of the compound of interest; (c) remove from the mass spectrum any peak that does not correspond to the compound of interest; and (d) replace the experimental m/z value for the peak identified in step (b) with a calculated theoretical m/z value for the ion fragment.

Abstract: A method of facilitating analysis of a peptide in a mass spectrometer comprising derivatizing the C-terminus of the peptide with an amino acid residue via a reaction with a carbodiimide reagent, yielding a derivative peptide, ionizing the derivative peptide with a double charge, and fragmenting the ionized derivative peptide in a mass spectrometry system, wherein binary fragments of the ionized derivative each include a charge, facilitating sequence analysis of the peptide.

Abstract: The present invention provides novel systems for sequencing nucleic acid molecules using dNTPs that are 3? end labeled with cleavable tags that block further extension and uniquely identify the bases to which they are attached. Removal of the tags liberates the 3? ends of the extension products for further extension. In related embodiments, oligonucleotides containing sequence-related cleavable tags are employed in a ligation reaction to determine the sequence of a particular DNA sample.

Abstract: The invention provides a system apparatus and methods for fragmenting various molecules. In particular, the invention may be employed for fragmenting biomolecules like peptides to determine sequence information. The invention provides a mass spectrometry system for photo-activated collision induced dissociation. The mass spectrometry system or device includes an ion source for producing ions, a photon source adjacent to the ion source for photo-activating ions produced by the ion source, an electrical element adjacent to the photon source for creating an electric field for accelerating ions produced by the ion source and photo-activated by the photon source; wherein ions are produced by the ion source, photo-activated by the photon source and accelerated into a surface to cause dissociation of the activated ions; and a detector downstream from the ion source for detecting the collision induced and dissociated ions.

Abstract: The present invention provides a new and improved method for quantitative determination and/or identification of proteins in a sample. In one aspect, the invention provides a mass spectroscopic method for comparing protein levels in two or more samples by differentially isotopically labeling each sample's proteins' N- or C-termini. In another aspect, the invention provides a mass-spectroscopic method for identifying a sample as source for a protein from a mixture of two or more samples by differentially isotopically labeling each sample's proteins' N- or C-termini.

Abstract: A method of analyzing a sample comprising multiple protein species is provided. The proteins are separated by species such that the multiple protein species emerge in a sequential order and are then digested in the sequential order in which they emerge from the separation process. The digested proteins are introduced into a mass spectrometer in the same sequential order so that, within a given time window, the digested proteins introduced into the mass spectrometer are covariant.

Abstract: The present invention provides an apparatus and method for use with a mass spectrometer. The multimode ionization source of the present invention provides one or more atmospheric pressure ionization sources (e.g., electrospray, atmospheric pressure chemical ionization and/or atmospheric pressure photoionization) for ionizing molecules. A method of producing ions using the multimode ionization source is also disclosed. The apparatus and method provide the advantages of the combined ion sources without the inherent disadvantages of the individual sources. In an embodiment, the multimode ionization source includes an infrared emitter enclosed in an inner chamber for drying a charged aerosol. ESI/APCI multimode sources may include a corona needle shield and/or an auxiliary electrode.

Abstract: An ion sampling apparatus for use in a mass spectrometry system. The ion sampling apparatus includes a target support for receiving a sample, an irradiation source for emitting energetic radiation or particles toward the target support, and a conduit having a curved end and a longitudinal axis, the curved end having an inlet with a central axis, the conduit being adjacent to the target support. The longitudinal axis of the conduit and the central axis of the inlet intersect to define an angle that is between about 20 degrees and about 210 degrees.

Abstract: The present invention provides a new and improved method for reducing the complexity of a proteomic sample, and preferably also for allowing identification of proteins in the sample. In one aspect, the invention provides a highly efficient method for identifying proteins in a proteomic sample by characterizing a single N-terminal peptide per protein. In another aspect, the invention provides a method for identifying proteins in a proteomic sample by characterizing a single C-terminal peptide per protein. In another aspect, the present invention provides a method for quantitative determination of differential protein expression and/or modification in different samples. In another aspect, the invention relates to kits useful for conveniently performing a method in accordance with the invention.

Abstract: The present invention relates to an apparatus for producing ions from an electrospray assembly. The apparatus comprises an ionization chamber, an electrospray assembly, an isolating electrode, an isolated ionization region within the ionization chamber and optionally, a vacuum interface at a vacuum interface voltage and a vacuum chamber. Sample is introduced into the ionization chamber from an electrospray assembly and transported to an electric field region that is isolated from the electric field created by the electrospray assembly.

Abstract: The invention provides a system apparatus and methods for fragmenting various molecules. In particular, the invention may be employed for fragmenting biomolecules like peptides to determine sequence information. The invention provides a mass spectrometry system for photo-activated collision induced dissociation. The mass spectrometry system or device includes an ion source for producing ions, a photon source adjacent to the ion source for photo-activating ions produced by the ion source, an electrical element adjacent to the photon source for creating an electric field for accelerating ions produced by the ion source and photo-activated by the photon source; wherein ions are produced by the ion source, photo-activated by the photon source and accelerated into a surface to cause dissociation of the activated ions; and a detector downstream from the ion source for detecting the collision induced and dissociated ions. Methods for molecule and/or peptide fragmentation are also disclosed.

Abstract: For generation and delivery of ions from an ionization chamber through an ion entrance orifice to a mass analyzer operating at high vacuum, high pass ion filtration is effected within the ionization chamber by application of electrical potentials to an electrode associated with the ion entrance orifice and to an electrode between the ionization region and the ion entrance orifice to create a retarding electric field upstream from the ion entrance orifice. The retarding electric field hinders the movement to the ion entrance orifice of ions having drift velocities below a lower limit, and as the retarding voltage gradient is made steeper, the lower limit increases.