PXD064279

PXD064279 is an original dataset announced via ProteomeXchange.

Title	n-Dodecyl-β-D-maltopyranoside (DDM)-Assisted Resolubilization Enhances Hydrophobic Peptide and Protein Identification in Bottom-Up Proteomics
Description	This study demonstrates that adding the non-ionic surfactant n-dodecyl-β-D-maltopyranoside (DDM) during protein resolubilization improves the identification of hydrophobic peptides and proteins in bottom-up proteomics. DDM's effectiveness in overcoming the challenge of losing hydrophobic proteins after precipitation from strong detergent lysis buffers was investigated. Using immortalized mouse macrophages (IMMs), DDM (0.05% or 0.1%) to resolubilization buffers, both with and without 8M urea in 50 mM ammonium bicarbonate (ABC) were added, for global and acyl-biotin exchange (ABE) proteomics (targeting S-palmitoylation). Key findings revealed that the addition of 0.1% DDM increased the identification of total peptides, proteins, and especially membrane-associated proteins in global proteomics compared to urea alone. Gene Ontology (GO) analysis showed that proteins uniquely identified with DDM were enriched in critical cellular processes. In ABE proteomics, 0.1% DDM enhanced the identification of hydrophobic and candidate S-palmitoylated peptides. DDM also increased the number of ABE-enriched proteins, with those uniquely identified by DDM being involved in cellular transport and localization known functions of S-palmitoylated proteins. In conclusion, incorporating DDM during protein resolubilization is a simple and effective method to enhance the coverage of hydrophobic proteomes in various bottom-up proteomics applications.
HostingRepository	PRIDE
AnnounceDate	2025-12-16
AnnouncementXML	Submission_2025-12-16_10:21:43.602.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Aleksandra Nita-Lazar
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	palmitoylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-25 20:47:05	ID requested
⏵ 1	2025-12-16 10:21:44	announced

10.1021/JASMS.5C00186;

submitter keyword: Macrophages, Protein resolubilization, Immunoproteomics,n-Dodecyl-β-D-maltopyranoside (DDM), Hydrophobic proteome, S-palmitoylation

Aleksandra Nita-Lazar
contact affiliation	National Institute of Allergy and Infectious Diseases, National Institutes of Health
contact email	nitalazarau@niaid.nih.gov
lab head
Aleksandra Nita-Lazar
contact affiliation	NIAID
contact email	nitalazarau@niaid.nih.gov
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD064279
     1. Label: PRIDE project
     2. Name: n-Dodecyl-β-D-maltopyranoside (DDM)-Assisted Resolubilization Enhances Hydrophobic Peptide and Protein Identification in Bottom-Up Proteomics