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公开(公告)号：WO2023064181A1
公开(公告)日：2023-04-20
申请号：PCT/US2022/046069
申请日：2022-10-07
摘要： A method of identifying an extant protein, including (a) providing inputs including: (i) a binding profile, wherein the binding profile includes a plurality of binding outcomes for binding of the extant protein to a plurality of different affinity reagents, wherein individual binding outcomes of the plurality of binding outcomes include a measure of binding between the extant protein and a different affinity reagent of the plurality of different affinity reagents, (ii) a database including information characterizing or identifying a plurality of candidate proteins, and (iii) a binding model; (b) determining a probability for each of the affinity reagents binding to each of the candidate proteins in the database according to the binding model; and (c) identifying the extant protein as a selected candidate protein having a probability for binding each of the affinity reagents that is most compatible with the binding profile for the extant protein.
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2.发明申请
公开(公告)号：WO2021252800A1
公开(公告)日：2021-12-16
申请号：PCT/US2021/036874
申请日：2021-06-10
发明人： EGERTSON, Jarrett D. , LOBANOV, Vadim , STERN, David , MALLICK, Parag , PATEL, Sujal M. , SEGHERS, Ryan K.
IPC分类号： G06K9/00 , G06K9/32 , C12Q1/6876 , G01N2021/6439 , G01N21/6428 , G06N20/00 , G06T2207/20081 , G06T2207/30072 , G06T7/0012 , G06T7/11 , G06V10/25 , G06V20/69
摘要： The present disclosure provides systems and methods for detecting components of an array of biological, chemical, or physical entities. In an aspect, the present disclosure provides a method for detecting an array of biological, chemical, or physical entities, comprising: (a) using one or more light sensing devices, acquiring pixel information from sites in an array, wherein the sites comprise biological, chemical, or physical entities that produce light; (b) processing the pixel information to identify a set of regions of interest (ROIs) corresponding to the sites in the array that produce the light; (c) classifying the pixel information for the ROIs into a categorical classification from among a plurality of distinct categorical classifications, thereby producing a plurality of pixel classifications; and (d) identifying one or more components of the array of biological, chemical, or physical entities based at least in part on the plurality of pixel classifications.
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公开(公告)号：WO2021087402A1
公开(公告)日：2021-05-06
申请号：PCT/US2020/058416
申请日：2020-10-30
IPC分类号： G01N33/543 , C09J5/02 , C09J5/04 , C03C27/06 , C07D487/04 , C07D237/26
摘要： Systems and methods for flow cells are provided. Flow cells may encompass a range of fluidic devices for various applications ranging from microfluidic systems to bulk phase flow systems. Flow cells may comprise one or more components for passive or active fluid transfer. Descriptions are provided for advantageous methods of fabricating flow cells for particular applications such as biological assays. Provided is a composition, comprising a first substrate comprising a first covalently -bound ligand; and a second substrate comprising a second covalently-bound ligand; wherein the first covalently-bound ligand and the second covalently-bound ligand are covalently bonded to form a heterocyclic compound. Also provided is a flow cell device, comprising: a first substrate comprising a microfabricated surface; and a second substrate comprising a non-pattemed surface; wherein the first substrate is joined to the second substrate to form an enclosure; and wherein the microfabricated surface comprises at least one chamber, wherein the chamber comprises a microarray of active sites with specific functionalization separated by an optically resolvable distance and a functionalized surface comprising a passivating group or a blocking group; and wherein each active site of the microarray of active sites comprises a capture agent.
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公开(公告)号：WO2021003470A1
公开(公告)日：2021-01-07
申请号：PCT/US2020/040829
申请日：2020-07-03
摘要： Methods and systems are provided for accurate and efficient identification and quantification of peptides. In an aspect, disclosed herein is a method for identifying a peptide in a sample of unknown peptides, comprising receiving information of a plurality of empirical measurements performed on the unknown peptides; comparing the information of empirical measurements against a database comprising a plurality of peptide sequences, each peptide sequence corresponding to a candidate peptide among a plurality of candidate peptides; and for each of one or more of the plurality of candidate peptides, generating a probability that the candidate peptide generates the information of empirical measurements, a probability that the plurality of empirical measurements is not observed given that the candidate peptide is present in the sample, or a probability that the candidate peptide is present in the sample; based on the comparison of the information of empirical measurements against the database.
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公开(公告)号：WO2023038859A1
公开(公告)日：2023-03-16
申请号：PCT/US2022/042499
申请日：2022-09-02
摘要： A method for characterizing proteins, including steps of (a) detecting a plurality of proteins, wherein individual proteins of the plurality are associated with unique identifiers, wherein the detecting distinguishes the identities of the individual proteins and the unique identifiers associated with the individual proteins; (b) digesting the proteins to form peptides, wherein the peptides from each protein are associated with the unique identifiers for the respective individual protein; (c) detecting the peptides and associated unique identifiers, wherein the detecting distinguishes characteristics of individual peptides, and wherein the detecting distinguishes unique identifiers associated with the individual peptides; and (d) correlating characteristics detected in step (c) with individual proteins detected in step (a) based on the unique identifiers associated with the individual proteins and the peptides.
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公开(公告)号：WO2022159520A2
公开(公告)日：2022-07-28
申请号：PCT/US2022/013017
申请日：2022-01-19
IPC分类号： G01N33/543 , G01N33/68 , G01N2440/00 , G01N33/6842 , G01N33/6845
摘要： Systems and methods for obtaining qualitative or quantitative measurements of proteoforms of polypeptides are described. The described methods include measurements of affinity reagent binding on single-molecule polypeptide arrays to distinguish between polypeptide isoforms. The described methods may provide high resolution quantitative comparisons of proteoforms with very low copy numbers.
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公开(公告)号：WO2023049073A1
公开(公告)日：2023-03-30
申请号：PCT/US2022/043987
申请日：2022-09-19
摘要： Methods and systems for identifying and/or quantifying polypeptide binding interactions of ligand-binding polypeptides are disclosed. Detailed methods include methods for identifying binding ligands of ligand-binding polypeptides and methods for assessing changes in binding behavior due to alterations of ligand-binding polypeptides. Detailed systems include array-based systems that permit detection of ligand binding interactions at single-analyte resolution.
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公开(公告)号：WO2023081728A1
公开(公告)日：2023-05-11
申请号：PCT/US2022/079181
申请日：2022-11-02
IPC分类号： C03C17/28 , B01J19/0046 , B01J2219/00608 , B01J2219/00637 , B01J2219/00711 , B01J2219/00725 , C03C2218/32 , C03C2218/328 , C03C2218/34
摘要： Systems and methods for the formation of single-analyte arrays are described. Array sites are formed via the patterning of surface-linked organic layers by electromagnetic radiation. Each array site may be modified after patterning to produce a chemistry at the array site that facilitates the controlled deposition of a single analyte at the array site.
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公开(公告)号：WO2020106889A1
公开(公告)日：2020-05-28
申请号：PCT/US2019/062482
申请日：2019-11-20
发明人： KLEIN, Josh , EGERTSON, Jarrett , CHAN, Tracy , TONAPI, Sonal , MALLICK, Parag , CHUNG, Minyong , OZER, Abdullah , SORELLE, Elliott , STERN, David
IPC分类号： C12N15/10 , C12N15/115 , C40B30/04 , C40B40/06 , G01N33/53
摘要： Methods and systems are provided herein for selecting an affinity reagent which binds a desired peptide epitope in a plurality of sequence contexts. The method relies on obtaining a peptide library, each peptide having the sequence αXβ, wherein X is the desired peptide epitope, wherein each of α and β comprise an amino acid, using the peptide library to select an affinity reagent.
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公开(公告)号：WO2022271983A1
公开(公告)日：2022-12-29
申请号：PCT/US2022/034780
申请日：2022-06-23
发明人： LOBANOV, Vadim , EGERTSON, Jarrett , WANG, Shunqiang , INDERMUHLE, Pierre , KAPP, Gregory , SEGHERS, Ryan , YOUSEFI, Siavash
IPC分类号： G16B40/30 , G16B30/00 , C12N15/1065 , G01N2021/6439 , G01N21/6428 , G01N21/643 , G01N33/68 , G01N33/6842 , G01N35/00613
摘要： Methods for performing procedures on single analytes at single-analyte resolution are disclosed. The methods utilize an iterative approach to performing a sequence of steps during a single-analyte process. Control of the single-analyte process is achieved by implementing actions during each iteration based upon one or more determined process metrics. Systems are also detailed for implementing the disclosed methods at single-analyte resolution.
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