PXD070700-1

PXD070700 is an original dataset announced via ProteomeXchange.

Title	Unveiling the unfolded proteome: evaluation and comparison of methods for the enrichment of intrinsically disordered proteins
Description	Intrinsically disordered proteins (IDPs) comprise a significant fraction of the eukaryotic proteome and are characterised by the absence of stable secondary or tertiary structures under physiological conditions. Despite their functional importance, comprehensive proteomic analysis of IDPs remains a challenge, mainly because they are poorly represented in conventional proteomics workflows. This underrepresentation is due to their susceptibility to proteolytic degradation, their limited crystallisability and, most critically, their lower abundance compared to structured proteins, which often dominate mass spectrometric analyses due to their higher solubility and stability. To address these limitations, we systematically evaluated and compared two widely used pre-fractionation methods: heat shock treatment (HEAT) and perchloric acid extraction (PCA). For structured proteins, harsh conditions such as elevated temperatures or extreme pH values induce denaturation, which exposes hydrophobic residues and leads to aggregation and precipitation. In contrast, IDPs, which are characterised by low hydrophobicity and an abundance of charged residues, generally remain soluble under these conditions. This different behaviour forms the basis for both enrichment strategies. Using MDA-MB-231 breast cancer cells as a model system, we have optimised and applied two extraction protocols: HEAT and PCA.
HostingRepository	PRIDE
AnnounceDate	2026-02-13
AnnouncementXML	Submission_2026-02-13_07:32:56.625.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD070700
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Giorgio Arrigoni
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 240

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-13 14:31:04	ID requested
⏵ 1	2026-02-13 07:32:58	announced

Secco L, Rocca G, Ingo AMD, Pobega E, Laera V, Manfioletti G, Arrigoni G, Sgarra R, Unveiling the unfolded proteome: Evaluation and comparison of methods for the enrichment of intrinsically disordered proteins. Protein Sci, 35(2):e70446(2026) [pubmed]

10.6019/PXD070700;

10.1002/pro.70446;

submitter keyword: heat extraction, LC-MS,Intrinsically Disordered Proteins, prefractionation methods, label-free quantification, perchloric acid extraction, disorder prediction algorithm, Instrinsically Disordered Proteins enrichment

Giorgio Arrigoni
contact affiliation	Department of Biomedical Sciences, University of Padova, Italy
contact email	giorgio.arrigoni@unipd.it
lab head
Giorgio Arrigoni
contact affiliation	University of Padova
contact email	giorgio.arrigoni74@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD070700
     1. Label: PRIDE project
     2. Name: Unveiling the unfolded proteome: evaluation and comparison of methods for the enrichment of intrinsically disordered proteins