Techniques for processing of mass spectral data

Patent metadata

Field	Value
Publication number	US-2018166265-A1
Application number	US-201615578148-A
Country	US
Kind code	A1
Filing date	May 31, 2016
Priority date	May 29, 2015
Publication date	Jun 14, 2018
Grant date	—

Abstract

Techniques for performing data acquisition and analysis are described. A multi-mode acquisition strategy may be performed which iteratively selects mass isolation windows of different sizes in different scan cycles to acquire experimental data. The mass isolation windows selected may provide for acquiring elevated energy scan data for a defined set of m/z values. Single scan data analysis may be performed. Data analysis may include forming precursor charge clusters, chaining precursor charge clusters having the same mass to charge ratio to form peaks profiles, and using criteria to align precursor and product ions of the experimental data. Unsupervised and supervised clustering may be performed using a database and composite ion spectra formed from experimental data. Also described are a small molecule acquisition enhancement and additional techniques applicable for biopharmaceutical and other applications.

First claim

1 - 96 . (canceled)

97 . A method of processing mass spectral data comprising:
performing an experiment using a sample, said experiment including performing mass analysis using a mass spectrometer; acquiring precursor ion data and fragment ion data as a result of performing the experiment; determining one or more precursor charge clusters included in the precursor ion data; performing peak detection for a first of the precursor charge clusters wherein the first precursor charge cluster is tracked across a plurality of scans forming a detected peak for the first precursor charge cluster; and determining, in accordance with validation criteria, a first set of fragment ions identified in the fragment ion data associated with the first precursor charge cluster.

98 . The method of claim 97 , wherein the method includes using the validation criteria to filter or refine an initial set of fragment ions, and determine a revised set of fragment ions.

99 . The method of claim 97 , wherein said mass spectrometer switches between a low energy mode generating primarily precursor ions and an elevated energy mode generating primarily fragment ions of the precursor ions, said switching being in accordance with a protocol that alternates application of the low energy mode and the elevated energy mode with a sufficient frequency whereby each of the low energy mode and the elevated energy mode is applied a plurality of times during a chromatographic peak width, wherein said precursor ion data is mass spectral data acquired when in the low energy mode and wherein said fragment ion data is mass spectral data acquired when in the elevated energy mode.

100 . The method of claim 97 , wherein each of the precursor charge clusters identifies a precursor ion at a single charge state.

101 . The method of claim 97 , wherein the validation criteria includes one or more intensity ratios of any of the first precursor charge cluster and a fragment ion of the first set of fragment ions.

102 . The method of claim 101 , wherein an apex scan is a scan at which the intensity of the first precursor charge cluster is at a maximum in the plurality of scans, and wherein said determining, in accordance with validation criteria, a first set of fragment ions identified in the fragment ion data associated with the first precursor charge cluster includes:
determining a first intensity ratio of the first precursor charge cluster in a first of the plurality of scans to the apex scan; determining a second intensity ratio of a first fragment ion of the first set in the first scan to the apex scan; and determining that the first intensity ratio and the second intensity ratio are approximately the same.

103 . The method of claim 97 , wherein the precursor ion data and fragment ion data is acquired from more than one mass isolation window across the plurality of scans.

104 . An apparatus comprising:
a processor; and a memory comprising code stored thereon that, when executed, performs a method of processing mass spectral data comprising:
performing an experiment using a sample, said experiment including performing mass analysis using a mass spectrometer;
acquiring precursor ion data and fragment ion data as a result of performing the experiment;
determining one or more precursor charge clusters included in the precursor ion data;
performing peak detection for a first of the precursor charge clusters wherein the first precursor charge cluster is tracked across a plurality of scans forming a detected peak for the first precursor charge cluster; and
determining, in accordance with validation criteria, a first set of fragment ions identified in the fragment ion data associated with the first precursor charge cluster.

105 . The apparatus of claim 104 , wherein the method includes using the validation criteria to filter or refine an initial set of fragment ions and determine a revised set of fragment ions.

106 . The apparatus of claim 104 , wherein said mass spectrometer switches between a low energy mode generating primarily precursor ions and an elevated energy mode generating primarily fragment ions of the precursor ions, said switching being in accordance with a protocol that alternates application of the low energy mode and the elevated energy mode with a sufficient frequency whereby each of the low energy mode and the elevated energy mode is applied a plurality of times during a chromatographic peak width, wherein said precursor ion data is mass spectral data acquired when in the low energy mode and wherein said fragment ion data is mass spectral data acquired when in the elevated energy mode.

107 . The apparatus of claim 104 , wherein each of the precursor charge clusters identifies a precursor ion at a single charge state.

108 . The apparatus of claim 104 , wherein the validation criteria includes one or more intensity ratios of any of the first precursor charge cluster and a fragment ion of the first set of fragment ions.

109 . The apparatus of claim 108 , wherein an apex scan is a scan at which the intensity of the first precursor charge cluster is at a maximum in the plurality of scans, and wherein said determining, in accordance with validation criteria, a first set of fragment ions identified in the fragment ion data associated with the first precursor charge cluster includes:
determining a first intensity ratio of the first precursor charge cluster in a first of the plurality of scans to the apex scan; determining a second intensity ratio of a first fragment ion of the first set in the first scan to the apex scan; and determining that the first intensity ratio and the second intensity ratio are approximately the same.

110 . The apparatus of claim 104 , wherein the precursor ion data and fragment ion data is acquired from more than one mass isolation window across the plurality of scans.

111 . A method of processing mass spectral data comprising:
performing an experiment using a sample, said experiment including performing mass analysis using a mass spectrometer, wherein said mass spectrometer operates in accordance with a schedule for a plurality of scans; acquiring, during a scan, precursor ion data within a mass isolation window; determining one or more precursor charge clusters using the precursor ion data;
adjusting the mass isolation window for a subsequent scan using the precursor ion data; and
determining a peak profile for a first precursor ion by chaining together a portion of the precursor charge clusters.

112 . The method of claim 111 , wherein said acquiring includes iteratively using different mass isolation windows in elevated energy scans.

113 . The method of claim 111 , including determining a bounded region having a plurality of dimensions including m/z and retention time; and iteratively using different mass isolation windows in elevated energy scans until fragmentation has been performed for the bounded region.

114 . The system of claim 111 , wherein said mass spectrometer switches between a low energy mode generating primarily precursor ions and an elevated energy mode generating primarily fragment ions of the precursor ions, said switching being in accordance with a protocol that alternates application of the low energy mode and the elevated energy mode with a sufficient frequency whereby each of the low energy mode and the elevated energy mode is applied a plurality of times during a chromatographic peak width, wherein said precursor ion data is mass spectral data acquired when in the low energy mode and wherein

Assignees

• Waters Technologies Corp

Inventors

• Geromanos Scott J
• Ciavarini Steven J
• Devlin Curt

Classifications

• G01N33/68

  involving proteins, peptides or amino acids {(involving lipoproteins G01N33/92)} · CPC title

• H01J49/0027

  Methods for using particle spectrometers · CPC title

• G01N30/72 Primary

  Mass spectrometers {(mass spectrometers per se H01J49/00)} · CPC title

• G16C20/70

  Machine learning, data mining or chemometrics · CPC title

• H01J49/0036 Primary

  Step by step routines describing the handling of the data generated during a measurement · CPC title