Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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).

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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).

Abstract: 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.

Abstract: 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.

Abstract: A method of performing tandem mass spectrometry (MS/MS) for identifying contents of a sample includes performing a mass spectrometry (MS) scan of the sample to obtain an MS/MS mass spectrum; identifying a first precursor ion species in the MS mass spectrum; performing an initial MS/MS scan of the first precursor ion species to obtain an initial MS/MS mass spectrum; and determining whether the initial MS/MS mass spectrum has a quality acceptable for peptide sequencing. When the first MS/MS mass spectrum has an unacceptable quality, the method further includes performing a subsequent MS/MS scan of the first precursor ion species to obtain a corresponding subsequent MS/MS mass spectrum of the first precursor ion species, and determining whether the subsequent MS/MS mass spectrum has a quality acceptable for peptide sequencing.

Abstract: 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.

Abstract: A system for detecting true peaks in a two-dimensional signal includes a two-dimensional separator and a processor. The two-dimensional separator is configured to perform separation of a sample to provide the two-dimensional signal. The processor is configured to identify candidate peaks of the two-dimensional signal based on local maxima of points on a surface defined by the two-dimensional signal, and to identify at least one true peak from the candidate peaks.