Identification and scoring of related compounds in complex samples

A method for verifying the retention time of a known compound using an adduct, modified form, or peptide of the known compound, comprising:

• obtaining a collection of product ion spectra for an entire mass range for a plurality of retention times, wherein a known compound and at least one adduct, modified form, or peptide of the known compound are separated from a sample mixture using a separation device and wherein one or more mass spectrometry/mass spectrometry (MS/MS) scans are performed on the separating sample mixture at each retention time of a plurality of retention times using one or more sequential precursor ion mass window widths in order to span the entire mass range, producing the collection of product ion spectra for the entire mass range for the plurality of retention times using a mass spectrometer;
• selecting M product ions of the known compound using a database that includes expected retention times and expected product ion mass spectra for the product ions of the known compound and the at least one adduct, modified form, or peptide of the known compound using a processor;
• calculating an extracted ion chromatogram (XIC) for each of the M product ions from the collection of product ion spectra using the processor, producing M XICs;
• calculating a first XIC peak group that represents the known compound from the M XICs using curve subtraction using the processor;
• selecting a first XIC peak of the first XIC peak group that represents the known compound using the processor;
• selecting L product ions of the at least one adduct, modified form, or peptide of the known compound using the database using the processor;
• calculating an XIC for each of the L product ions from the collection of product ion spectra using the processor, producing L XICs;
• calculating a second XIC peak group that represents the at least one adduct, modified form, or peptide of the known compound from the L XICs using curve subtraction using the processor;
• selecting a second XIC peak of the second XIC peak group that represents the at least one adduct, modified form, or peptide of the known compound using the processor;
• shifting the retention time of the second XIC peak by the difference between the expected retention time of the first XIC peak found from the database and the expected retention time of the second XIC peak found from the database using the processor;
• and
• verifying that the retention time of the first XIC peak is the retention time of the known compound if the shifted retention time of the second XIC peak is within a retention time threshold of the retention time of the first XIC peak using the processor.

A computer program product, comprising a non-transitory and tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for verifying the retention time of a known compound using an adduct, modified form, or peptide of the known compound, the method comprising:

• providing a system, wherein the system comprises one or more distinct software modules, and wherein the distinct software modules comprise a measurement module and an analysis module;
• obtaining a collection of product ion spectra for an entire mass range for a plurality of retention times using the measurement module, wherein a known compound and at least one adduct, modified form, or peptide of the known compound are separated from a sample mixture using a separation device and wherein one or more mass spectrometry/mass spectrometry (MS/MS) scans are performed on the separating sample mixture at each retention time of a plurality of retention times using one or more sequential precursor ion mass window widths in order to span the entire mass range, producing the collection of product ion spectra for the entire mass range for the plurality of retention times using a mass spectrometer;
• selecting M product ions of the known compound using a database that includes expected retention times and expected product ion mass spectra for the product ions of the known compound and the at least one adduct, modified form, or peptide of the known compound using the analysis module;
• calculating an extracted ion chromatogram (XIC) for each of the M product ions from the collection of product ion spectra using the analysis module, producing M XICs;
• calculating a first XIC peak group that represents the known compound from the M XICs using curve subtraction using the analysis module;
• selecting a first XIC peak of the first XIC peak group that represents the known compound using the analysis module;
• selecting L product ions of the at least one adduct, modified form, or peptide of the known compound using the database using the analysis module;
• calculating an XIC for each of the L product ions from the collection of product ion spectra using the analysis module, producing L XICs;
• calculating a second XIC peak group that represents the at least one adduct, modified form, or peptide of the known compound from the L XICs using curve subtraction using the analysis module;
• selecting a second XIC peak of the second XIC peak group that represents the at least one adduct, modified form, or peptide of the known compound using the analysis module;
• shifting the retention time of the second XIC peak by the difference between the expected retention time of the first XIC peak found from the database and the expected retention time of the second XIC peak found from the database using the analysis module;
• and
• verifying that the retention time of the first XIC peak is the retention time of the known compound if the shifted retention time of the second XIC peak is within a retention time threshold of the retention time of the first XIC peak using the analysis module.