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Owen Leddy, Yufei Cui, Ryuhjin Ahn, Lauren Stopfer, Elizabeth Choe, Do Hun Kim, Malte Roerden, Stefani Spranger, Bryan D. Bryson & Forest M. White
DOI: https://www.nature.com/articles/s41596-024-01076-x#Sec43
Abstract: Vaccines and immunotherapies that target peptide–major histocompatibility complexes (peptide–MHCs) have the potential to address multiple unmet medical needs in cancer and infectious disease. Designing vaccines and immunotherapies to target peptide–MHCs requires accurate identification of target peptides in infected or cancerous cells or tissue, and may require absolute or relative quantification to identify abundant targets and measure changes in presentation under different treatment conditions. Internal standard parallel reaction monitoring (also known as ‘SureQuant’) can be used to validate and/or quantify MHC peptides previously identified by using untargeted methods such as data-dependent acquisition. SureQuant MHC has three main use cases: (i) conclusive confirmation of the identities of putative MHC peptides via comparison with an internal synthetic stable isotope labeled (SIL) peptide standard; (ii) accurate relative quantification by using pre-formed heavy isotope-labeled peptide–MHC complexes (hipMHCs) containing SIL peptides as internal controls for technical variation; and (iii) absolute quantification of each target peptide by using different amounts of hipMHCs loaded with synthetic peptides containing one, two or three SIL amino acids to provide an internal standard curve. Absolute quantification can help determine whether the abundance of a peptide–MHC is sufficient for certain therapeutic modalities. SureQuant MHC therefore provides unique advantages for immunologists seeking to confidently validate antigenic targets and understand the dynamics of the MHC repertoire. After synthetic standards are ordered (3–4 weeks), this protocol can be carried out in 3–4 days and is suitable for individuals with mass spectrometry experience who are comfortable with customizing instrument methods.
SEEK ID: https://fairdomhub.org/studies/1353
Projects: Cancer Systems Biology Consortium (CSBC)
Study position:
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Created: 19th Mar 2025 at 17:38
Last updated: 19th Mar 2025 at 18:01

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- Samples (144)
Projects: Hi-IMPAcTB, MIT SRP, MetNet, Endometriosis, Cancer Systems Biology Consortium (CSBC)
Institutions: Massachusetts Institute of Technology
Projects: MIT SRP, Hi-IMPAcTB, MetNet, Endometriosis, Cancer Systems Biology Consortium (CSBC)
Web page: https://nextseek.mit.edu/
Programme: NExtSEEK
Public web page: Not specified
Organisms: Not specified
Submitter: Charles Demurjian
Studies: Structural and systems characterization of phosphorylation on metabolic ..., Validation and quantification of peptide antigens presented on MHCs usin...
Assays: All Metadata, ImmunoPeptideomics - Data Linked, Sample Processing - Metadata, SureQuant Analysis - Data Linked
Snapshots: No snapshots
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: CSBC
Organisms: No organisms
SOPs: P.WHI-250319-V1_SureQuant_SampleProcessing.docx
Data files: samples-publish250319_CEL.xlsx, samples-publish250319_TIS.xlsx
Snapshots: No snapshots
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: CSBC
Organisms: No organisms
SOPs: P.WHI-250319-V1_SureQuant_Protocol.pdf
Data files: samples-publish250319_CEL.xlsx, samples-publish250319_CHM.xlsx, samples-publish250319_D.MSP.xlsx
Snapshots: No snapshots
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: CSBC
Organisms: No organisms
SOPs: P.WHI-250319-V1_SureQuant_Protocol.pdf
Data files: samples-publish250319_A.MSP.xlsx, samples-publish250319_D.MSP.xlsx
Snapshots: No snapshots
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: CSBC
Organisms: No organisms
SOPs: No SOPs
Data files: SureQuant - AllMetadata.xlsx
Snapshots: No snapshots
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: CSBC
Studies: Validation and quantification of peptide antige...
Assays: All Metadata
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: CSBC
Studies: Validation and quantification of peptide antige...
Assays: SureQuant Analysis - Data Linked
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: CSBC
Studies: Validation and quantification of peptide antige...
Assays: ImmunoPeptideomics - Data Linked, SureQuant Analysis - Data Linked
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: CSBC
Studies: Validation and quantification of peptide antige...
Assays: ImmunoPeptideomics - Data Linked
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: CSBC
Studies: Validation and quantification of peptide antige...
Assays: ImmunoPeptideomics - Data Linked, Sample Processing - Metadata
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: CSBC
Studies: Validation and quantification of peptide antige...
Assays: Sample Processing - Metadata
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: CSBC
Studies: Validation and quantification of peptide antige...
Assays: ImmunoPeptideomics - Data Linked, SureQuant Analysis - Data Linked
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: CSBC
Studies: Validation and quantification of peptide antige...
Assays: Sample Processing - Metadata