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US 2026/0029401 A1Published application
Methods and systems for characterizing proteoforms of significant proteins of interest
AssigneeNautilus Subsidiary, Inc.
InventorsParag MALLICK, Andreas HUHMER, Kara JUNEAU, Vivekananda BUDAMAGUNTA, Grant NAPIER
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Abstract
Methods, reagents, kits and systems for analyzing different proteoforms of proteins of interest are provided. The provided methods, systems, etc. provide detection, characterization and quantitation of proteoforms for different biologically relevant proteins for monitoring and characterizing biological processes.
Claims40
A method of analyzing proteins in a first sample, comprising:
- providing a population of individual protein molecules from the first sample wherein said individual protein molecules are individually addressable, and wherein the population of individual molecules comprises a plurality of individual molecules of at least one protein of interest selected from catenin beta 1, mitogen activated protein kinase 1 (ERK2), epidermal growth factor receptor (EGFR), receptor tyrosine kinase erbB-2 (HER2), leucine rich repeat serine/threonine-protein kinase 2 (LRRK2), RAC-alpha serine/threonine protein kinase (AKT1), and Mothers against decapentaplegic homolog 2 protein (SMAD2);
- identifying a proteoform of the at least one protein of interest represented by each of the plurality of individual molecules of the at least one protein of interest based upon identification of a presence or absence of at least 3 different modifications within each of the individual molecules of the at least one protein of interest;
- and
- characterizing a plurality of proteoforms of the at least one protein of interest present in the sample.
1 more element
A system for characterizing proteins, comprising:
- one or more solid supports comprising molecules of at least one protein of interest immobilized thereon, wherein the at least one protein of interest is selected from catenin beta 1, mitogen activated protein kinase 1 (ERK2), epidermal growth factor receptor (EGFR), receptor tyrosine kinase erbB-2 (HER2), leucine rich repeat serine/threonine-protein kinase protein 2 (LRRK2), RAC-alpha serine/threonine protein kinase (AKT1), and Mothers against decapentaplegic homolog 2 protein (SMAD2) proteins, and wherein individual molecules of the at least one protein of interest are individually addressable;
- a source of a plurality of different affinity reagents, each different affinity reagent having a binding affinity to the at least one protein of interest having a different modification;
- a fluidic system for delivering the plurality of different affinity reagents to the one or more solid supports to contact the affinity reagents with the individual molecules of the at least one protein of interest;
- a detector for detecting whether each of the different affinity reagents binds to individual molecules of the at least one protein of interest;
- a processor programed to characterize proteoforms of the at least one protein of interest present on the one or more solid supports from detected binding or nonbinding of the different affinity reagents to the individual molecules of the at least one protein of interest.
2 more elements
An array, comprising:
- a plurality of individual molecules of at least one protein of interest deposited on a surface of the array and positioned to be individually addressable, wherein the at least one protein of interest is selected from catenin beta 1, mitogen activated protein kinase 1 (ERK2), epidermal growth factor receptor (EGFR), receptor tyrosine kinase erbB-2 (HER2), leucine rich repeat serine/threonine-protein kinase protein 2 (LRRK2), RAC-alpha serine/threonine protein kinase (AKT1), and Mothers against decapentaplegic homolog 2 protein (SMAD2), and wherein, and wherein the plurality of individual molecules of the at least one protein of interest comprises at least two proteoforms of the at least one protein of interest;
- and
- a first affinity reagent having binding specificity for at least a first characteristic of at least one of the two proteoforms of the at least one protein of interest, the first affinity reagent being bound to individual molecules of the at least one protein of interest possessing the first characteristic of at least one of the two proteoforms of the at least one protein of interest.
A library of reagents, comprising:
- a plurality of sources of affinity reagents, where each source of the plurality of sources contains a separate affinity reagent;
- and wherein each affinity reagent:
- has a binding specificity for a different characteristic of one or more proteoforms of at least one protein of interest selected from catenin beta 1, mitogen activated protein kinase 1 (ERK2), epidermal growth factor receptor (EGFR), receptor tyrosine kinase erbB-2 (HER2), leucine rich repeat serine/threonine-protein kinase protein 2 (LRRK2), RAC-alpha serine/threonine protein kinase (AKT1), and Mothers against decapentaplegic homolog 2 protein (SMAD2);
- and
- a detectable label attached to the affinity reagent.
2 more elements
Dependencies are inferred from the claim text.