Dataset Information

Unveiling the unfolded proteome: evaluation and comparison of methods for the enrichment of intrinsically disordered proteins

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

SUBMITTER: Giorgio Arrigoni

LAB HEAD: Giorgio Arrigoni

PROVIDER: PXD070700 | Pride | 2026-02-13

REPOSITORIES: Pride

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Unveiling the unfolded proteome: Evaluation and comparison of methods for the enrichment of intrinsically disordered proteins.

Secco Luca L Rocca Giulia G Ingo Alberto Maria Davide AMD Pobega Enrico E Laera Valentina V Manfioletti Guidalberto G Arrigoni Giorgio G Sgarra Riccardo R

Protein science : a publication of the Protein Society 20260201 2

Intrinsically disordered proteins (IDPs) represent a family of proteins that given their structural peculiarity, that is, absence of defined secondary or tertiary structures, are very flexible and display great adaptability in binding to other molecules. For these reasons, IDPs are often key nodes in modulatory molecular networks. While 3D-structured proteins undergo aggregation and precipitation in denaturing conditions, due to the exposure of their hydrophobic core to the aqueous environment, ...[more]

PMID: 41556566

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	Heat1_TR1_HighSens.raw	Raw
	Heat1_TR2_HighSens.raw	Raw
	Heat2_TR1_HighSens.raw	Raw
	Heat2_TR2_HighSens.raw	Raw
	Heat3_TR1_HighSens.raw	Raw