Abstract: A method comprises: (1) making an extract of a biological sample; (2) repeatedly: (a) choosing a respective one of a plurality of pre-determined protein or polypeptide analyte compounds; (b) introducing a portion of the extract into an electrospray ionization source, thereby generating positive ions comprising a plurality of ion species; (c) isolating a plurality of subsets of the ion species comprising respective mass-to-charge (m/z) ratio ranges, each range including an m/z ratio corresponding to a respective protonation state of the chosen compound; (d) reacting the isolated plurality of subsets of first-generation ion species with proton transfer reaction reagent anions for a pre-determined time duration; (e) generating a mass spectrum of the product ion species; and (g) identifying either the presence or absence of the compound based on the mass spectrum; and (3) identifying the presence or absence of the microorganism within the sample based on analytes present.

Abstract: A method comprises: (1) making an extract of a biological sample; (2) repeatedly: (a) choosing a respective one of a plurality of pre-determined protein or polypeptide analyte compounds; (b) introducing a portion of the extract into an electrospray ionization source, thereby generating positive ions comprising a plurality of ion species; (c) isolating a plurality of subsets of the ion species comprising respective mass-to-charge (m/z) ratio ranges, each range including an m/z ratio corresponding to a respective protonation state of the chosen compound; (d) reacting the isolated plurality of subsets of first-generation ion species with proton transfer reaction reagent anions for a pre-determined time duration; (e) generating a mass spectrum of the product ion species; and (g) identifying either the presence or absence of the compound based on the mass spectrum; and (3) identifying the presence or absence of the microorganism within the sample based on analytes present.

Abstract: Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (PTR) are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kDa by removing charge and reducing the collisional cross section.

Abstract: Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (PTR) are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kDa by removing charge and reducing the collisional cross section.

Abstract: A mass spectrometry system arrangement includes a curved ion guide, where the curve of the ion guide is positioned such that a portion of the ion optics are visible from at the ion guide entrance, e.g. line of sight or z-axis. There are four electrodes parallel with each other and the central curved axis. Each electrode is equally radially spaced from the curved central axis. For each cross section of the ion guide, the central curved axis being positioned at the origin, the curved electrodes being radially positioned at 45°, 135°, 225°, and 315°. Depending upon the system, a blocking device is positioned external to the ion guide but within the “line of sight” or positioned tangential to the rising section of the bent ion guide.

Abstract: A mass spectrometry system arrangement includes a curved ion guide, where the curve of the ion guide is positioned such that a portion of the ion optics are visible from at the ion guide entrance, e.g. line of sight or z-axis. There are four electrodes parallel with each other and the central curved axis. Each electrode is equally radially spaced from the curved central axis. For each cross section of the ion guide, the central curved axis being positioned at the origin, the curved electrodes being radially positioned at 45°, 135°, 225°, and 315°. Depending upon the system, a blocking device is positioned external to the ion guide but within the “line of sight” or positioned tangential to the rising section of the bent ion guide.

Abstract: An ion processing apparatus includes a plurality of electrodes, first and second insulators, a housing, and a plurality of compliant first supports and second supports. Each electrode has a length along a central axis, and includes a first end region and an axially opposing second end region. The first and second insulators are coaxially disposed about the first and second end regions, respectively. The housing is coaxially disposed about the electrodes, the first insulator and the second insulator. The first supports extend between, and into contact with, the first insulator and the housing. The second supports extend between, and into contact with, the second insulator and the housing. The supports isolate the electrodes from external forces.

Abstract: An ion processing apparatus includes a plurality of electrodes, first and second insulators, a housing, and a plurality of compliant first supports and second supports. Each electrode has a length along a central axis, and includes a first end region and an axially opposing second end region. The first and second insulators are coaxially disposed about the first and second end regions, respectively. The housing is coaxially disposed about the electrodes, the first insulator and the second insulator. The first supports extend between, and into contact with, the first insulator and the housing. The second supports extend between, and into contact with, the second insulator and the housing. The supports isolate the electrodes from external forces.

Abstract: In some embodiments, a method of optimizing operating parameters of an analytical instrument (e.g. lens voltages of a mass spectrometer) includes steps taken to minimize the method duration in the presence of substantial instrument noise and/or drift. Some methods include selecting a best point between a default instrument parameter set (vector) and a most-recent optimum parameter set; building a starting simplex at the selected best point location in parameter-space; and advancing the simplex to find an optimal parameter vector. The best simplex points are periodically re-measured, and the resulting readings are used to replace and/or average previous readings. The algorithm convergence speed may be adjusted by reducing simplex contractions gradually. The method may operate using all-integer parameter values, recognize parameter values that are out of an instrument range, and operate under the control of the instrument itself rather than an associated control computer.

Abstract: In some embodiments, a tandem (MS/MS) mass spectrometry method includes selecting a collision-induced dissociation (CID) voltage amplitude and a q-parameter value for a quadrupole ion trap to optimize a daughter ion fragmentation process for a given parent ion mass-to-charge (m/z) ratio. The q and CID voltage values may be selected according to a look-up table and/or using approximate analytical expressions. The correspondence between m/z values and (q, CID) value pairs may be established by pre-measurement calibration. A fragmentation-optimized q value may be computed according to m/z, and a CID voltage value may be determined according to the computed q value. A user may also force q to another value, for example in order to facilitate trapping of a desired daughter ion mass range, and the controller computes a CID voltage value according to the forced q value.

Abstract: In some embodiments, a tandem (MS/MS) mass spectrometry method includes selecting a collision-induced dissociation (CID) voltage amplitude and a q-parameter value for a quadrupole ion trap to optimize a daughter ion fragmentation process for a given parent ion mass-to-charge (m/z) ratio. The q and CID voltage values may be selected according to a look-up table and/or using approximate analytical expressions. The correspondence between m/z values and (q, CID) value pairs may be established by pre-measurement calibration. A fragmentation-optimized q value may be computed according to m/z, and a CID voltage value may be determined according to the computed q value. A user may also force q to another value, for example in order to facilitate trapping of a desired daughter ion mass range, and the controller computes a CID voltage value according to the forced q value.

Abstract: In some embodiments, a method of optimizing operating parameters of an analytical instrument (e.g. lens voltages of a mass spectrometer) includes steps taken to minimize the method duration in the presence of substantial instrument noise and/or drift. Some methods include selecting a best point between a default instrument parameter set (vector) and a most-recent optimum parameter set; building a starting simplex at the selected best point location in parameter-space; and advancing the simplex to find an optimal parameter vector. The best simplex points are periodically re-measured, and the resulting readings are used to replace and/or average previous readings. The algorithm convergence speed may be adjusted by reducing simplex contractions gradually. The method may operate using all-integer parameter values, recognize parameter values that are out of an instrument range, and operate under the control of the instrument itself rather than an associated control computer.