{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2026:UEYB77AJBYH6T2A4DN6LU7RFGF","short_pith_number":"pith:UEYB77AJ","canonical_record":{"source":{"id":"2605.21084","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"physics.bio-ph","submitted_at":"2026-05-20T12:20:42Z","cross_cats_sorted":[],"title_canon_sha256":"f0cf052c1a6f31d96d59b215c332510b83c1a9215d789450a333e6202bce830e","abstract_canon_sha256":"5d39dfa895657f2c89824ba6db172dc6e7d9c77ded8e83273aa1f35842f98b94"},"schema_version":"1.0"},"canonical_sha256":"a1301ffc090e0fe9e81c1b7cba7e25314da4cfba13d9e91e13cdd45ea2d9e7a7","source":{"kind":"arxiv","id":"2605.21084","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2605.21084","created_at":"2026-05-21T01:05:36Z"},{"alias_kind":"arxiv_version","alias_value":"2605.21084v1","created_at":"2026-05-21T01:05:36Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2605.21084","created_at":"2026-05-21T01:05:36Z"},{"alias_kind":"pith_short_12","alias_value":"UEYB77AJBYH6","created_at":"2026-05-21T01:05:36Z"},{"alias_kind":"pith_short_16","alias_value":"UEYB77AJBYH6T2A4","created_at":"2026-05-21T01:05:36Z"},{"alias_kind":"pith_short_8","alias_value":"UEYB77AJ","created_at":"2026-05-21T01:05:36Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2026:UEYB77AJBYH6T2A4DN6LU7RFGF","target":"record","payload":{"canonical_record":{"source":{"id":"2605.21084","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"physics.bio-ph","submitted_at":"2026-05-20T12:20:42Z","cross_cats_sorted":[],"title_canon_sha256":"f0cf052c1a6f31d96d59b215c332510b83c1a9215d789450a333e6202bce830e","abstract_canon_sha256":"5d39dfa895657f2c89824ba6db172dc6e7d9c77ded8e83273aa1f35842f98b94"},"schema_version":"1.0"},"canonical_sha256":"a1301ffc090e0fe9e81c1b7cba7e25314da4cfba13d9e91e13cdd45ea2d9e7a7","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-21T01:05:36.195175Z","signature_b64":"jOBavU96aWqUGzASl1aPhzkCSc7iadkxMwTCTQbKOG6+2C5YjBZeR3OwZ5LYRREVQkUOhmbc5fgBVWgd82hOCg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"a1301ffc090e0fe9e81c1b7cba7e25314da4cfba13d9e91e13cdd45ea2d9e7a7","last_reissued_at":"2026-05-21T01:05:36.194401Z","signature_status":"signed_v1","first_computed_at":"2026-05-21T01:05:36.194401Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2605.21084","source_version":1,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-21T01:05:36Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"kr80cn+pYHp7qEWsRqcaXcbVRMsWBT+749T3mZfjWVLrWQ2UVTkWDqz9ZLDDUNlZfLvdzzZ7gW7lC32lUJEZBw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-26T05:56:30.684458Z"},"content_sha256":"b08073cb3a20768149df5162c8331de0e3d7df94f1d3481442900d23f9f4f109","schema_version":"1.0","event_id":"sha256:b08073cb3a20768149df5162c8331de0e3d7df94f1d3481442900d23f9f4f109"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2026:UEYB77AJBYH6T2A4DN6LU7RFGF","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Label-free SERS Discrimination of Native Proline Hydroxylation at Single-molecule peptide by Deep Learning-assisted plasmonic nanopore","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"physics.bio-ph","authors_text":"Enock Adjei Agyekum, Francesco De Angelis, Jianan Huang, Kuo Zhan, Matti Putkonen, Pei-Lin Xin, Shuai Li, Yingqi Zhao, Yuge Liang","submitted_at":"2026-05-20T12:20:42Z","abstract_excerpt":"Post-translational modifications (PTMs) play essential roles in regulating protein structure, function, and cellular signalling. However, peptide level discrimination of hydroxylation at the single-molecule level remains difficult. Here, we report a particle-in-pore single-molecule surface-enhanced Raman spectroscopy (SERS) platform combined with peak occurrence frequency (POF) analysis and a one-dimensional convolutional neural network (1D-CNN) for discriminating hydroxylated and non-hydroxylated HIF peptide fragments. Three peptide pairs containing the Pro-564 hydroxylation site, with length"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2605.21084","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2605.21084/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-21T01:05:36Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"CVuzcmlzDjyd8JhQPMY1jyJRpaSLqW/QgwCGAs/rFoD9wI8uUMqu1OW0B97EIEQeQ2sHCLF6u5laaZkGqcblCg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-26T05:56:30.685210Z"},"content_sha256":"b69419cc559980e36f9b9de0fdeb470d5bc6127e6b3ad6a48d0672289e08086e","schema_version":"1.0","event_id":"sha256:b69419cc559980e36f9b9de0fdeb470d5bc6127e6b3ad6a48d0672289e08086e"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/UEYB77AJBYH6T2A4DN6LU7RFGF/bundle.json","state_url":"https://pith.science/pith/UEYB77AJBYH6T2A4DN6LU7RFGF/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/UEYB77AJBYH6T2A4DN6LU7RFGF/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-05-26T05:56:30Z","links":{"resolver":"https://pith.science/pith/UEYB77AJBYH6T2A4DN6LU7RFGF","bundle":"https://pith.science/pith/UEYB77AJBYH6T2A4DN6LU7RFGF/bundle.json","state":"https://pith.science/pith/UEYB77AJBYH6T2A4DN6LU7RFGF/state.json","well_known_bundle":"https://pith.science/.well-known/pith/UEYB77AJBYH6T2A4DN6LU7RFGF/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2026:UEYB77AJBYH6T2A4DN6LU7RFGF","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"5d39dfa895657f2c89824ba6db172dc6e7d9c77ded8e83273aa1f35842f98b94","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"physics.bio-ph","submitted_at":"2026-05-20T12:20:42Z","title_canon_sha256":"f0cf052c1a6f31d96d59b215c332510b83c1a9215d789450a333e6202bce830e"},"schema_version":"1.0","source":{"id":"2605.21084","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2605.21084","created_at":"2026-05-21T01:05:36Z"},{"alias_kind":"arxiv_version","alias_value":"2605.21084v1","created_at":"2026-05-21T01:05:36Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2605.21084","created_at":"2026-05-21T01:05:36Z"},{"alias_kind":"pith_short_12","alias_value":"UEYB77AJBYH6","created_at":"2026-05-21T01:05:36Z"},{"alias_kind":"pith_short_16","alias_value":"UEYB77AJBYH6T2A4","created_at":"2026-05-21T01:05:36Z"},{"alias_kind":"pith_short_8","alias_value":"UEYB77AJ","created_at":"2026-05-21T01:05:36Z"}],"graph_snapshots":[{"event_id":"sha256:b69419cc559980e36f9b9de0fdeb470d5bc6127e6b3ad6a48d0672289e08086e","target":"graph","created_at":"2026-05-21T01:05:36Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"integrity":{"available":true,"clean":true,"detectors_run":[],"endpoint":"/pith/2605.21084/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Post-translational modifications (PTMs) play essential roles in regulating protein structure, function, and cellular signalling. However, peptide level discrimination of hydroxylation at the single-molecule level remains difficult. Here, we report a particle-in-pore single-molecule surface-enhanced Raman spectroscopy (SERS) platform combined with peak occurrence frequency (POF) analysis and a one-dimensional convolutional neural network (1D-CNN) for discriminating hydroxylated and non-hydroxylated HIF peptide fragments. Three peptide pairs containing the Pro-564 hydroxylation site, with length","authors_text":"Enock Adjei Agyekum, Francesco De Angelis, Jianan Huang, Kuo Zhan, Matti Putkonen, Pei-Lin Xin, Shuai Li, Yingqi Zhao, Yuge Liang","cross_cats":[],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"physics.bio-ph","submitted_at":"2026-05-20T12:20:42Z","title":"Label-free SERS Discrimination of Native Proline Hydroxylation at Single-molecule peptide by Deep Learning-assisted plasmonic nanopore"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2605.21084","kind":"arxiv","version":1},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:b08073cb3a20768149df5162c8331de0e3d7df94f1d3481442900d23f9f4f109","target":"record","created_at":"2026-05-21T01:05:36Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"5d39dfa895657f2c89824ba6db172dc6e7d9c77ded8e83273aa1f35842f98b94","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"physics.bio-ph","submitted_at":"2026-05-20T12:20:42Z","title_canon_sha256":"f0cf052c1a6f31d96d59b215c332510b83c1a9215d789450a333e6202bce830e"},"schema_version":"1.0","source":{"id":"2605.21084","kind":"arxiv","version":1}},"canonical_sha256":"a1301ffc090e0fe9e81c1b7cba7e25314da4cfba13d9e91e13cdd45ea2d9e7a7","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"a1301ffc090e0fe9e81c1b7cba7e25314da4cfba13d9e91e13cdd45ea2d9e7a7","first_computed_at":"2026-05-21T01:05:36.194401Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-21T01:05:36.194401Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"jOBavU96aWqUGzASl1aPhzkCSc7iadkxMwTCTQbKOG6+2C5YjBZeR3OwZ5LYRREVQkUOhmbc5fgBVWgd82hOCg==","signature_status":"signed_v1","signed_at":"2026-05-21T01:05:36.195175Z","signed_message":"canonical_sha256_bytes"},"source_id":"2605.21084","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:b08073cb3a20768149df5162c8331de0e3d7df94f1d3481442900d23f9f4f109","sha256:b69419cc559980e36f9b9de0fdeb470d5bc6127e6b3ad6a48d0672289e08086e"],"state_sha256":"215e7a1d9055f998c6ca73bd47d162e97bf2db743f6db0e9b17ba0f43a2342ed"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"NbuT9Ccazyv97mp/74Cz57SYmcnoEJQt9X6Fr+0zXahWYQuNDQIYC9H4hFfGpqny3j9zp9X/QR65aRv3TfIQDA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-26T05:56:30.689478Z","bundle_sha256":"f6438a1ed51b67debc2f6780efde372ed96923f07819aa284b5f3813cbfb13e4"}}