Proteomics

Dataset Information

0

EpiProfile 2.0: a proteomics tool to quantify histone modifications by mass spectrometry


ABSTRACT: The histone LC-MS/MS data analysis is challenging due to the large number and variety of isobaric histone peptides, and the high dynamic range of histone peptide abundances. We introduce EpiProfile 2.0 to quantify histone post-translational modifications from mass spectrometry data, in which fragment ions are used to determine the retention time of peptides and discriminate isobaric peptides. EpiProfile can automatically recognize and efficiently process both data-dependent and data-independent acquisition runs (DDA and DIA), and high-resolution and low-resolution instrument runs. The proteomics tool was tested on human cells and validated by synthetic histone peptides. EpiProfile is the first automatic program to determine the retention time and discriminate isobaric peptides for histone modifications with DIA MS.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Hela Cell

DISEASE(S): Cervix Carcinoma

SUBMITTER: Zuo-Fei Yuan  

LAB HEAD: Benjamin A. Garcia

PROVIDER: PXD004166 | Pride | 2018-05-29

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
1histone_6.par Other
1histone_CIDIT_histonetest.mgf Mgf
1histone_F002262.dat Other
1histone_F002262.dat-pride.pride.mgf.gz Mgf
1histone_F002262.dat-pride.pride.mztab.gz Mztab
Items per page:
1 - 5 of 23
altmetric image

Publications

EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data.

Yuan Zuo-Fei ZF   Sidoli Simone S   Marchione Dylan M DM   Simithy Johayra J   Janssen Kevin A KA   Szurgot Mary R MR   Garcia Benjamin A BA  

Journal of proteome research 20180530 7


Epigenetics has become a fundamental scientific discipline with various implications for biology and medicine. Epigenetic marks, mostly DNA methylation and histone post-translational modifications (PTMs), play important roles in chromatin structure and function. Accurate quantification of these marks is an ongoing challenge due to the variety of modifications and their wide dynamic range of abundance. Here we present EpiProfile 2.0, an extended version of our 2015 software (v1.0), for accurate q  ...[more]

Similar Datasets

2015-03-27 | PXD001541 | Pride
2022-02-07 | PXD018295 | Pride
2014-09-01 | PXD001118 | Pride
2016-06-01 | PXD003709 | Pride
2008-07-22 | E-GEOD-11102 | biostudies-arrayexpress
2019-08-27 | PXD011198 | Pride
2022-05-06 | PXD031767 | Pride
2023-08-30 | PXD020326 | Pride
2016-06-16 | PXD002560 | Pride
2022-04-04 | PXD028269 | Pride