PXD024745

PXD024745 is an original dataset announced via ProteomeXchange.

Title	Comparison of in-gel digestion methods for histone PTM analysis
Description	In order to optimize the histone digestion procedure for low-abundance clinical samples, we compared different in-gel digestion protocols. Histones are usually digested in-gel using “Arg-C-like” strategies, which involve chemical acylation of lysines followed by trypsin digestion (17). Acylated lysines are not recognized by trypsin, which -as a consequence- cuts only at the C-terminus of arginines and generates peptides of suitable length for MS analysis. We compared four Arg-C-like protocols: 1) D3 protocol (deuterated acetic anhydride as acylating agent); 2) PRO protocol (propionic anhydride as acylating agent); 3) PRO-PRO protocol (propionic anhydride as acylating agent and peptide N-terminal derivatization); 4) PRO-PIC protocol (propionic anhydride as acylating agent and phenyl-isocyanate as peptide N-terminal derivatization). We also used an Arg-C in solution digestion as a reference, and tested the performance of the methods with decreasing sample amounts.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_13:38:02.396.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Roberta Noberini
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; acetylated residue; dimethylated residue; N6,N6,N6-trimethyl-L-lysine
Instrument	Q Exactive HF; Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-15 08:24:26	ID requested
⏵ 1	2024-10-07 13:38:03	announced

Noberini R, Savoia EO, Brandini S, Greco F, Marra F, Bertalot G, Pruneri G, McDonnell LA, Bonaldi T, Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples. Clin Epigenetics, 13(1):145(2021) [pubmed]

10.1186/s13148-021-01120-7;

ProteomeXchange project tag: EPIC-XS

submitter keyword: epigenetics,histone post-translationa modification

Tiziana Bonaldi
contact affiliation	European Institute of Oncology
contact email	tiziana.bonaldi@ieo.it
lab head
Roberta Noberini
contact affiliation	Istituto Europeo di Oncologia
contact email	roberta.noberini@ieo.it
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD024745

PRIDE project URI

• PRIDE
  1. PXD024745
     1. Label: PRIDE project
     2. Name: Comparison of in-gel digestion methods for histone PTM analysis