Agilent Technologies, Inc.

Javier E Satulovsky

Joel Myerson

Brian Phillip Smart

Gregory Staples

Craig Daniel Wenger

Magdalena Anna Bynum

Systems, computer-readable media, and methods using mass spectrometry to analyze a sample are provided. For example, a method includes: acquiring a precursor ion spectrum; analyzing the precursor ion spectrum to identify precursor ions that preliminarily match one or more peptides that each belong to at least one protein of interest for the analysis; selecting each of the identified precursor ions in an order according to a ranking protocol for maximizing the number of proteins that are identified in the sample; for each selected precursor ion: acquiring a corresponding product ion spectrum, determining whether the acquired product ion spectrum matches one of the peptides that belong to the set of proteins of interest, and identifying a matched peptide as being present in the sample; and identifying proteins of interest that are present in the sample based on the peptides that are identified as being present in the sample.

System and method of data-dependent acquisition by mass spectrometry

Systems and method for mass spectrometry are presented. In one embodiment, a method comprises: (a) acquiring one or more fragmentation signatures for a reference sample, wherein each fragmentation signature of the reference sample is acquired with a unique tandem mass spectrometry mode; (b) identifying one or more discriminate features across the plurality of fragmentation signatures of the reference sample; (c) acquiring one or more fragmentation signatures for an unknown sample, wherein each fragmentation signature of the unknown sample is acquired according to the discriminant features of step (b); (d) identifying one or more discriminate features across the plurality of fragmentation signatures of the unknown sample; (e) scoring the fragmentation signatures of step (c) by comparing the discriminate features of the reference sample, from step (b), against the discriminate features of the unknown sample, from step (d); and (f) identifying a structural isomer based on the score of step (e).

Method for isomer discrimination by tandem mass spectrometry

Compound tags and shifting agents are provided that find use in ion mobility spectrometry (IMS), mass spectrometry (MS), or a combination of IMS and MS, and which can substantially increase separation of multiple components in complex samples and facilitate quantitative and multiplexed analyses. In some cases, the compounds include a linker and a normalizing group, each including a structural unit and separated by a cleaveable group, and a crown ether. Also provided are methods for analyzing peptides in a sample. In some cases, the method includes coupling the compound to peptides which include a terminal guanidinium moiety capable of forming an intra-molecular complex with the crown ether.

Ion mobility mass spectrometry tags for quantitative applications and methods thereof

A system for performing tandem mass spectrometry (MS/MS) analysis of a sample includes a mass spectrometer and a processor. The mass spectrometer is configured to perform a mass spectrometry (MS) scan of an ionized sample to provide a mass of an observed peak corresponding to a precursor ion. The processor is configured to perform operations including determining whether the mass of the observed peak matches a mass of at least one of multiple expected peptides on a dynamic watch list, where the expected peptides correspond to a protein in the sample, and calculating a score of an accuracy of the determination when the mass of the observed peak is determined to match the mass of at least one of the plurality of expected peptides. The precursor ion is excluded from an MS/MS scan when the accuracy score indicates that the determination is accurate.

System and method for performing tandem mass spectrometry analysis

A system for estimating a baseline of a signal exhibits a signal generator and a processor. The signal generator is configured to generate a signal exhibiting a plurality of peaks and a baseline. The processor is configured to perform operations including determining an estimator indicating at least one region of the signal that exhibits a peak, determining a weight indicating at least one region of the signal that does not exhibit a peak based on the estimator, and estimating the baseline of the signal based on at least the determined weight.

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Santa Clara, CA, United States of America

Javier E Satulovsky