PXD057918-1

PXD057918 is an original dataset announced via ProteomeXchange.

Title	Protein sequencing with single amino acid resolution discerns peptides that discriminate tropomyosin proteoforms
Description	Protein variants of the same gene—proteoforms—can have high molecular similarity yet exhibit different biological functions. Thus, identifying unique peptides that unambiguously map to proteoforms can provide crucial biological insights. In humans, four human tropomyosin (TPM) genes produce similar proteoforms that can be challenging to distinguish with standard proteomics tools. For example, TPM1 and TPM2 share 85% sequence identity, with amino acid substitutions that play unique roles in muscle contraction and myopathies. In this study, we evaluated the ability of the recently released Platinum single-molecule protein sequencer to detect proteoform-informative peptides. Platinum employs fluorophore-labeled recognizers that reversibly bind to cognate N-terminal amino acids (NAAs), enabling polypeptide sequencing within nanoscale apertures of a semiconductor chip that can accommodate single peptide molecules. As a proof of concept, we evaluated the ability of Platinum to distinguish three main types of proteoform variation: paralog-level, transcript-level, and post-translational modification (PTM). We distinguished paralogous TPM1 and TPM2 peptides differing by a single isobaric residue (leucine/isoleucine). We also distinguished tissue-specific TPM2 spliceforms. Notably, we found that a phosphotyrosine-modified peptide displayed reduced recognizer affinity for tyrosine, showing sensitivity to PTMs. This study paves the way for the targeted detection of proteoform biomarkers at the single molecule level.
HostingRepository	PanoramaPublic
AnnounceDate	2025-09-03
AnnouncementXML	Submission_2025-09-03_08:43:09.848.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Erin Jeffery
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Phospho; Delta:H(2)C(2)
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-14 21:23:44	ID requested
⏵ 1	2025-09-03 08:43:10	announced

Sittipongpittaya N, Skinner KA, Jeffery ED, Watts EF, Sheynkman GM, Protein Sequencing with Single Amino Acid Resolution Discerns Peptides That Discriminate Tropomyosin Proteoforms. J Proteome Res, 24(8):3798-3807(2025) [pubmed]

submitter keyword: Amino acid variant, single-molecule peptide sequencing, tropomyosin, genetic variants, alternative splicing, phosphorylation, recognizer-based sequencing, proteoforms, isobaric peptides, proteogenomics

Gloria Sheynkman
contact affiliation	University of Virginia Dept of Molecular Biology and Biological Physics
contact email	gs9yr@virginia.edu
lab head
Erin Jeffery
contact affiliation	University of Virginia Dept of Molecular Biology and Biological Physics
contact email	edf4n@virginia.edu
dataset submitter

Panorama Public dataset URI