Provided herein are single-substance multi-point calibration techniques for quantitative mass spectrometry using the theoretical relative abundance of isotopes in a calibrator. Also provided herein are methods of determining the concentration of an analyte using a calibrator for the analyte.

A method of mass spectrometry for analyzing a sample within a mass range of interest includes the steps: ionizing the sample to produce a plurality of precursor ions; performing an MS1 scan of the precursor ions comprising mass analyzing the precursor ions across the mass range of interest, to obtain an MS1 mass spectrum of the precursor ions; determining ion intensity values within the MS1 mass spectrum; selecting precursor mass segments within the mass range of interest, and for each precursor mass segment: fragmenting the precursor ions within that precursor mass segment; and performing an MS2 scan of the fragmented ions by: controlling an amount of fragmented ions for that precursor mass segment, based on an intensity value for that precursor mass segment derived from the MS1 spectrum; and mass analyzing the amount of fragmented ions.

A system and method to screen a plurality of molecules in datasets obtained from mass spectroscopy, including selecting and receiving at least one dataset of mass spectral data, and selecting customizable m/z mass tolerance peaks to assign initial compound assignments from at least one adduct ion hierarchy database for at least one compound having a parent molecule. Adduct ion hierarchy screening is applied to at least a portion of the dataset, wherein selected dataset features are tested to determine if they represent the most abundant expected adduct of the parent molecule class and if the expected adduct assignment hierarchy are present in the dataset.

The present invention relates to methods and products associated with in vivo enzyme profiling. In particular, the invention relates to methods of in vivo processing of exogenous molecules followed by detection of signature molecules as representative of the presence of active enzymes associated with diseases or conditions. The invention also relates to products, kits, and databases for use in the methods of the invention.

The invention relates to the analysis of carbohydrates, such as N-glycans and O-glycans found on proteins. The invention relates, in part, to glycan labeling with formulas/compounds enhancing their detection and/or analysis by methods such as capillary electrophoresis, liquid chromatography and mass spectrometry. These detection methods may be useful in studying glycosylation patterns of biological or medical samples, or for assessing protein production, protein quality/purity, for comparing innovator and biosimilar glycosylated proteins, or for selecting proteins with the desired glycosylation.

Described are methods, compositions, and devices for a concatemeric protein standard that behaves as a protein but transforms into single peptides upon digestion, which is optimized to function as a non-obtrusive process control for mass spectrometry analysis.

A method for diagnosing a disease, such as breast cancer, in a biological sample using spectroscopic data is described. The method involves computer-implemented method that runs an algorithm. The algorithm converts spectroscopic vibrational from the sample into a profile, and scores the profile using a pair of reference profiles. Based on the score and a threshold, it can be determined whether the subject from which the sample was obtained has a disease, and, if so, to what extent. The method also allows detection of early and pre-disease states in subjects based on the detection of signal of low concentration analytes that are indicative of early or incipient disease state. The method is non-invasive, non-subjective, and highly specific and sensitive. The method affords the application of a single standard of diagnostic accuracy, independent of the local availability of expert pathologists.

The current disclosure provides antibodies that bind to peptides associated with the primary immunodeficiency disorders (PIDD) Wiskott-Aldrich Syndrome (WAS) and X-linked agammaglobulinemia (XLA). The antibodies can be used in peptide immunoaffinity enrichment coupled to selected reaction monitoring mass spectrometry (immuno-SRM) assays for clinical diagnosis and newborn screening of WAS and XLA, among other uses.

Methods for derivatization of biomolecules including glycans or other biopolymers with one or more fluorescent, MS active compounds by reductive amination or rapid tagging in order to produce derivatized glycan having a pKa >7 and between about 200 Å and about 1000 Å of nonpolar surface area are described.

Methods of treating a cancer in a patient are provided. The methods can include obtaining a tumor sample from a patient, detecting whether CCNG1 gene expression is present in the tumor sample, diagnosing the patient with a CCNG1 inhibitor-responsive cancer when the presence of CCNG1 gene expression in the tumor sample is detected, and/or administering an effective amount of a CCNG1 inhibitor to the diagnosed patient. CCNG1 inhibitors can include a viral vector having a binding peptide that is configured to bind one or more signature (SIG) elements of an invading tumor and at least one cytocidal gene. CCNG1 inhibitors including cell penetrating peptides are also provided.