Comprehensive proteome and phosphoproteome profiling shows negligible influence of RNAlater on protein abundance and phosphorylation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31049047", "kind": "science-record", "revision": 7, "content_hash": "sha256:fe434a27988f06605e75bcf782c3fc88189d3f6e4ac6a7e99d24321d676c9feb", "created_at": "2026-11-01T15:40:44Z", "updated_at": "2026-11-01T22:00:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive proteome and phosphoproteome profiling shows negligible influence of RNAlater on protein abundance and phosphorylation.", "doi": "10.1186/s12014-019-9239-z", "pmid": "31049047", "authors": ["Jingi Bae", "Su-Jin Kim", "Seung-Eun Lee", "Wooil Kwon", "Hongbeom Kim", "Youngmin Han", "Jin-Young Jang", "Min-Sik Kim", "Sang-Won Lee"], "journal": "Clinical proteomics", "year": 2019, "abstract": "Certain tumors such as pancreatic ductal adenocarcinoma (PDAC) are known to contain a variety of hydrolytic enzymes including RNases and proteases that may lead to degradation of RNA and proteins during sample processing. For such tumor tissues with RNA instability, RNAlater containing a high concentration of quaternary ammonium sulfates that denature RNA-hydrolyzing enzymes is often used to protect RNAs from hydrolysis. Although a few studies have been carried out to determine the effect of RNAlater on DNA and RNA, whether RNAlater influences the proteome and phosphoproteome is largely unknown. In this study we carried out a systematic and comprehensive analysis of the effect of RNAlater on the proteome and phosphoproteome using high-resolution mass spectrometry. PDAC tissues from three patients were individually pulverized and the tissue powders of each patient were divided into two portions, one of which was incubated in RNAlater at 4 °C for 24 h (RNAlater tissue) while the other was kept at - 80 °C (frozen tissue). Comprehensive quantitative profiling experiments on the RNAlater tissues and the frozen tissues resulted in the identification of 99,136 distinct peptides of 8803 protein groups and 17,345 phosphopeptides of 16,436 phosphosites. The data exhibited no significant quantitative changes in both proteins and phosphorylation between the RNAlater tissues and the frozen tissue. In addition, the phosphoproteome data showed heterogeneously activated pathways among the three patients that were not altered by RNAlater. These results indicate that the tissue preservation method using RNAlater can be effectively used on PDAC tissues for proteogenomic studies where preservation of intact DNA, RNA and proteins is prerequisite. 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Password: 7dRc2zNt).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Comprehensive evaluation of RNAlater effect on proteome and phosphoproteome", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31049047:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:15929884700f532b37207692a9955ec6511dd873bdb8605ce98af7a0a9d58d68", "bytes": 599, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#Tab1", "version": null, "note": "Four phosphopeptides found to be significantly altered by RNAlater", "structure": {"pmcid": "PMC6482574", "section_index": 15, "section_title": "Comparison of variations in proteome and phosphoproteome across patient tissues with variations induced by RNAlater", "row_count": 5, "column_count": 6}, "table": {"label": "Table 1", "caption": "Four phosphopeptides found to be significantly altered by RNAlater", "rows": [["Protein ID", "Gene symbol", "Amino acid", "Position within protein", "Localization probability", "Sequence window"], ["P84101", "SERF2", "S", "21", "0.95", "QRELARQKNMKKQSDSVKGKRRDDGLSAAAR"], ["P05114", "HMGN1", "S", "89", "0.99", "LPAENGETKTEESPASDEAGEKEAKSD___"], ["Q7RTV5", "AAED1", "S", "12", "1", "___MAAPAPVTRQVSGAAALVPAPSGPDSG"], ["Q07002", "CDK18", "S", "12", "0.99", "___MNKMKNFKRRFSLSVPRTETIEESLAE"]], "row_count": 5, "column_count": 6, "numeric_cells": 12, "header_rows": 1, "locator": "section[15]/table-wrap[1]#Tab1"}}], "gaps": ["asset:data:geo:PXD010710 not downloaded", "asset:data:geo:PXD010710 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Fold changes induced by RNAlater were calculated and p values were estimated based on Student t test"}}], "targets": [], "gaps": ["method.student_t"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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