The present disclosure provides methods for determining the amount of FXN or FXN fusion protein in a sample, e.g, a tissue sample, by using mass spectrometry.

The invention relates generally to peptide biomarkers with specific ionization characteristics to directly quantify one or more target HPPD proteins in biological samples, including crop plant samples, by liquid chromatography coupled tandem mass spectrometry multiple reaction monitoring (MRM). The peptide biomarkers in combination with MRM-based methods may be used to quantify a single target protein or multiple target proteins within a crop plant, such as maize, utilizing selected peptide biomarkers either alone or in combination. The present disclosure allows for broad based, reliable quantitation in different biological matrices, including plant matrices. Also provided are different peptide biomarker combinations that can be used to perform the methods of the invention.

The invention pertains to chemoselective sensitivity booster for tagging a peptide, peptide conjugate, or similar reactive molecule for analysis of a peptide, protein, antibody, protein bioconjugate, antibody bioconjugate, and similar analytes. The sensitivity booster comprises of sp2 or sp3 nitrogen centers in combination with hydrophobic carbon chains linked with an electrophile or nucleophile for attachment with a peptide, peptide conjugate, or molecules with similar reactivity.

A method of evaluating a function of an organ for transplantation harvested from a living body, the method includes preparing data representing change over time in content of marker substances in accordance with a perfusion, taking a first tissue sample from the organ for transplantation at first timing in a reperfusion of the organ for transplantation, taking a second tissue sample from the organ for transplantation at second timing after the first timing in the reperfusion, measuring contents of the marker substances in the first tissue sample, measuring contents of the marker substances in the second tissue sample, calculating change in content at the second timing as compared with the first timing for each of the marker substances, and calculating an indicator relating to evaluation of the function of the organ for transplantation using the calculated change in content and the data.

Provided herein are methods of identifying structures, e.g., attributes, of a therapeutic protein or a target that affect an interaction between the therapeutic protein and the target. In exemplary embodiments, the method comprises: (a) applying a stress to a first sample comprising therapeutic proteins or targets; (b) contacting the first sample with a second sample comprising targets or therapeutic proteins to form a mixture comprising (i) therapeutic protein-target complexes, (ii) unbound therapeutic proteins, and (iii) unbound targets; and (c) separating the mixture into at least two fractions, wherein an unbound fraction comprises unbound therapeutic proteins or unbound targets and a bound fraction comprises therapeutic protein-target complexes; and (d) for each of the unbound fraction and bound fraction, identifying and quantifying the abundance of the structures, e.g., attribute, present on a species of the therapeutic protein or target.

A method, apparatus, and computer-readable medium for adaptive normalization of analyte levels in one or more samples, the method including receiving one or more analyte levels corresponding to one or more analytes detected in the one or more samples, each analyte level corresponding to a detected quantity of that analyte in the one or more samples; and iteratively applying a scale factor to the one or more analyte levels over one or more iterations until a change in the scale factor between consecutive iterations is less than or equal to a predetermined change threshold or until a quantity of the one or more iterations exceeds a maximum iteration value, each iteration in the one or more iterations comprising: determining a distance between each analyte level in the one or more analyte levels and a corresponding reference distribution of that analyte in a reference data set; determining the scale factor based at least in part on analyte levels that are within a predetermined distance of their corresponding reference distributions; and normalizing the one or more analyte levels by applying the scale factor.

The methods disclosed herein employ unique combinations of processing steps that transform a blood or CSF sample into a sample suitable for quantifying MTBR tau species, as well as other tau species. The present disclosure also encompasses the use of MTBR tau species in blood or CSF to measure pathological features and/or clinical symptoms of 3R- and 4R-tauopathies in order to diagnose, stage, and/or choose treatments appropriate for a given disease stage, and modify a given treatment regimen.

The present invention relates to the field of protein post-translational modification. More specifically, the present invention provides compositions and methods useful for identifying O-linked glycosylation sites in proteins. In one embodiment, the present invention provides a method for identifying O-linked glycosylation sites of Tn antigen in proteins comprising the steps of (a) digesting proteins present in a sample into peptides; (b) enriching for Tn-glycopeptides; (c) conjugating Tn-glycopeptides to solid phase; (d) labeling Tn using the glycosyltransferse enzyme C1GalT1 and a labeled uridine diphosphate galactose (UDP-Gal) substrate to produce labeled Tn-glycopeptides; (e) releasing the labeled Tn-glycopeptides from the solid-phase using an endopeptidase that cleaves peptides at the N-terminus of O-linked glycans at serine or threonine residues; and (f) mapping O-linked glycosylation sites of Tn antigen using liquid chromatography-mass spectrometry.

Methods and apparatuses for the identification and/or characterization of properties of a macromolecule based on mass spectrometry data. Specifically, described herein are methods and apparatuses for converting peptide-level data into a pseudo-intact mass spectra. Also described herein are methods and apparatuses for converting peptide-level data into a pseudo-electropherogram. The methods may be well suited for analyzing proteins and protein complexes, including estimating properties of post-translational modifications of the proteins and protein complexes. Methods may include generating a theoretical graph or spectrum based on peptide-level mass spectrometry data. In some embodiments, the theoretical graph may be a theoretical intact mass spectrum or a theoretical charge distribution spectrum.

An improved chemical probe for the detection of the amino acid citrulline combines: 1) a reactive head formed of 1,3-dicarbonyl moiety that reacts with a citrulline side chain in an improved manner compared to currently used 1,2-dicarbonyl moieties; and 2) a modular action of the probe where citrulline side chains are labeled first using reactive heads described above, and attachment of a read-out subunit or tag, be it a fluorophore, a nanoparticle, or an antigen is performed separately. The modular nature of the chemical probe increases the sensitivity of the probes due to their smaller size. Additionally, the chemical probes of the present disclosure allow the same sample to be analyzed using a variety of read-out methods.