Browse
Submit Data
Databases
API
Help

Dataset Information

575 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Histione HCD and CID datasets for evaluation of search engines

ABSTRACT: To identify confident spectra from histone peptides containing PTMs, we present a method in which one kind of modification is searched each time. We then combine the identifications of multiple search engines to obtain confident results. We find that two search engines, pFind and Mascot, identify most of the confident results. This study will be beneficial those who are interested in histone proteomics analysis.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): T Cell, Cell Culture

SUBMITTER: Zuo-Fei Yuan

LAB HEAD: Benjamin A. Garcia

PROVIDER: PXD001118 | Pride | 2014-09-01

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	1HCD_Histone.mgf	Mgf
	1HCD_Histone.raw	Raw
	1HCD_Histone_1.dat	Other
	1HCD_Histone_1.dat-pride.pride.mgf.gz	Mgf
	1HCD_Histone_1.dat-pride.pride.mztab.gz	Mztab

Items per page:

1 - 5 of 72

Publications

Evaluation of proteomic search engines for the analysis of histone modifications.

Yuan Zuo-Fei ZF Lin Shu S Molden Rosalynn C RC Garcia Benjamin A BA

Journal of proteome research 20140907 10

Identification of histone post-translational modifications (PTMs) is challenging for proteomics search engines. Including many histone PTMs in one search increases the number of candidate peptides dramatically, leading to low search speed and fewer identified spectra. To evaluate database search engines on identifying histone PTMs, we present a method in which one kind of modification is searched each time, for example, unmodified, individually modified, and multimodified, each search result is ...[more]

PMID: 25167464

Similar Datasets

Quantifying histone PTMs by bottom-up MS

Project description:Histone post-translational modifications (PTMs) contribute to chromatin function through their chemical properties which influence chromatin structure, and their ability to recruit chromatin interacting proteins. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry (nanoLC-MS/MS) has emerged as the most suitable technology for global histone modification analysis due to the high sensitivity and the high mass accuracy that provide confident identification. However, the histone nanoLC-MS/MS data analysis is even more challenging due to the large number and variety of isobaric histone peptides, and the high dynamic range of histone peptide abundances. Here, we introduce EpiProfile, a software tool that discriminates isobaric histone peptides using the distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. The accuracy of EpiProfile was evaluated by analysis of mixtures containing different ratios of synthetic histone peptides. In addition to label-free quantification of histone peptides, EpiProfile is flexible, and can quantify different types of isotopically labeled histone peptides. EpiProfile is much more convenient when compared to manual quantification, filling the need of an automatic and freely available tool to quantify labeled and non-labeled modified histone peptides. In summary, EpiProfile is a valuable nanoLC-MS/MS based quantification tool for histone modifications, which can also be adapted to analyze non-histone protein samples.

2015-03-27 | PXD001541 | Pride

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

Project description: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.

2018-05-29 | PXD004166 | Pride

Chromatin profiling in human neurons reveals aberrant roles for histone acetylation and BET family proteins in schizophrenia

Project description:Schizophrenia (SZ) is a psychiatric disorder with complex genetic risk dictated by interactions between hundreds of risk variants. Epigenetic factors, such as histone posttranslational modifications (PTMs), have been shown to play critical roles in many neurodevelopmental processes, and when perturbed may also contribute to the precipitation of disease. Here, we apply an unbiased proteomics approach to evaluate combinatorial histone PTMs in human induced pluripotent stem cell (hiPSC)-derived forebrain neurons from individuals with SZ. We observe hyper-acetylation of H2A.Z and H4 in neurons derived from SZ cases, results that were confirmed in postmortem human brain. We demonstrate that the bromodomain and extraterminal (BET) protein, BRD4, is a bona fide ‘reader’ of H2A.Z acetylation, and further provide evidence that BET family protein inhibition ameliorates transcriptional abnormalities in patient-derived neurons. Thus, treatments aimed at alleviating BET protein interactions with hyperacetylated histones may aid in the prevention or treatment of SZ.

2022-05-06 | PXD031767 | Pride

Preferential phosphorylation on old histones during early mitosis in human cells

Project description:How histone posttranslational modifications (PTMs) are inherited through cell cycle remains poorly understood. Canonical histones are made in the S phase of cell cycle. Combining mass spectrometry-based technologies and stable isotope labeling by amino acids in cell culture (SILAC), we interrogate the distributions of multiple major histone PTMs on old versus new histones in synchronized human cells. We show that histone PTMs can be grouped to three categories accordingly to their distributions. Most lysine mono-methylation and acetylation PTMs are either symmetrically distributed on old and new histones, or asymmetric on new histones. In contrast, most di- and tri-methylation PTMs are asymmetric on old histones, suggesting the inheritance of different PTMs is regulated distinctly. Intriguingly, old and new histones are distinguished in their phosphorylation status during early mitosis, in three different human cell types: Hela, 293T and human foreskin fibroblast (HFF) cells. The mitotic hallmark H3S10ph is predominantly associated with old H3 at early mitosis and become symmetric with the progression of mitosis. The same distribution pattern is found on other mitotic histone phosphorylation marks, including H3T3/T6ph, H3.1/2S28ph and H1.4S26ph, excluding S28/S31ph on the H3 variant H3.3. Although H3S10ph often associates with the neighboring K9 di- or tri-methylation, they are not required for the asymmetric distribution of S10ph on the same H3 tail. Inhibition of the kinase Aurora B does not change the distribution pattern despite significant reduction of H3S10ph levels. K9me2 abundance on the new H3 is significantly reduced after Aurora B inhibition, suggesting a crosstalk between H3S10ph and H3K9me2.

2016-06-01 | PXD003709 | Pride

Genome-wide distribution maps of histone variants H2A.Lap1 and H2A.Z in 30do mouse spermatids [ChIP_seq]

Project description:Chromatin performs numerous functions during cellular differentiation, and therefore it must be capable of adopting a multitude of different structures. How these various structures are established is poorly understood, but we propose that specific histone H2A variants will have a key role in remodelling chromatin during differentiation. Structurally, we show here that the gain of just a single acidic amino acid residue has generated a new mouse H2A.Bbd-like histone variant, H2A.Lap1, and that when incorporated into nucleosomal arrays imparts on them unique biophysical properties that are distinct from arrays containing either H2A or human H2A.Bbd. Functionally, we identify H2A.Lap1 as a novel chromatin component of active genes that are expressed during spermatogenesis, and in combination with H2A.Z create a unique chromatin landscape at the start site of transcription. During round spermatid differentiation, H2A.Lap1 dramatically loads onto the inactive X chromosome enabling a subset of its genes to be transcriptionally activated Examination of 2 different histone variants in mouse spermatids.

2012-01-20 | E-GEOD-29913 | biostudies-arrayexpress

Hemi-methylated DNA regulates DNA methylation inheritance through allosteric control of H3 ubiquitylation by UHRF1

Project description:DNA methylation is a heritable chromatin modification essential to mammalian development that functions with histone post-translational modifications to regulate chromatin structure and gene expression programs. The epigenetic inheritance of DNA methylation requires the combined actions of DNMT1 and UHRF1, a histone- and DNA-binding RING E3 ubiquitin ligase that facilitates DNMT1 recruitment to sites of newly replicated DNA through the ubiquitylation of histone H3. UHRF1 binds DNA with modest selectivity towards hemi-methylated CpG dinucleotides (HeDNA); however, the contribution of HeDNA sensing to UHRF1 function remains elusive. Here, we reveal that the interaction of UHRF1 with HeDNA is required for DNA methylation inheritance but is dispensable for chromatin interaction, which is governed by reciprocal positive cooperativity between the UHRF1 histone- and DNA-binding domains. We further show that HeDNA functions as an allosteric regulator of UHRF1 ubiquitin ligase activity, directing ubiquitylation towards multiple lysines on the H3 tail adjacent to the UHRF1 histone-binding site. Collectively, our studies define a highly orchestrated epigenetic control mechanism involving modifications both to histones and DNA that facilitate UHRF1 chromatin targeting, H3 ubiquitylation, and DNA methylation inheritance.

2016-08-25 | PXD003983 | Pride

Functional studies of a H2A.Bbd-like histone variant in mouse spermatogenesis

Project description:This SuperSeries is composed of the following subset Series: GSE29781: Expression data from 30do mouse spermatids [Affymetrix] GSE29913: Genome-wide distribution maps of histone variants H2A.Lap1 and H2A.Z in 30do mouse spermatids[ChIP_seq] Refer to individual Series

2012-01-20 | E-GEOD-29916 | biostudies-arrayexpress

Comparison of genome-wide DNA methylation in MEFs derived from wildtype or estrogen receptor beta null mice using reduced representation bisulfite sequencing

Project description:Estrogen receptor beta (ERÎ²) is a ligand inducible transcription factor regulating gene expression in response to the female sex hormone estrogen. Previously, we found that ERÎ² deficiency results in changes in DNA methylation patterns at two gene promoters, implicating an involvement of ERÎ² in DNA methylation. In this study, we set out to explore this involvement on a genome-wide level, and to investigate the underlying mechanisms of this function. Using reduced representation bisulfite sequencing (RRBS), we compared genome-wide DNA methylation in mouse embryonic fibroblasts (MEFs) derived from wildtype (wt) and ERÎ² knock-out (Î²erko) mice, and identified around 8000 differentially methylated positions (DMPs). This suggests that ERÎ² is involved in regulating DNA methylation at specific sites in the genome. Genome-wide DNA methylation was analysed in MEFs derived from wildtype and ERbeta null mice by educed representation bisulfite sequencing (RRBS) on an Illumina Genome Analyser IIx platform.

2016-02-22 | E-GEOD-72230 | biostudies-arrayexpress

Coupling SDS-PAGE to capillary zone electrophoresis-tandem mass spectrometry for high-resolution top-down proteomics analysis of intact histone proteoforms

Project description:Top-down mass spectrometry (TDMS) is a powerful tool to reveal the mechanism of epigenetic regulation by histones. However, the high similarity of histone variants and their highly dynamic post-translational modifications (PTMs) make them as on-going challenge analytes for separation with traditional chromatographic-based methods. Sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE), which enables high-resolution protein separation based on molecular size, not only split histone proteins in different channels, but also isolate the large intact histone proteins from the truncated ones. Here, for the first time, we employed SDS-PAGE integrating with the second-dimensional separation of capillary zone electrophoresis (CZE) to distinguish intact histone proteoforms containing different PTMs. Due to the unique physicochemical property of histone proteins regarding small proteins carrying highly positive charges, we systematically evaluated every step in the strategy, achieving high histone protein recovery with trichloroacetic acid precipitation, better separation with basic sample buffer as well as confident identification with low collision energy for histone proteins. The optimized workflow provides the distinguish of intact histone variants that differ by few amino acids near both the N- and C-termini as well as the identification of combinatorial PTMs and the crosstalk between PTMs.

2024-10-15 | PXD048061 | Pride

N-terminome profiling in HEK293T

Project description:Various forms of the protein, called proteoform, are generated by co- or post-translational modification, alternative splicing and alternative translation initiation site, resulting in interactions between ribosomes, mRNAs, tRNAs, and various enzymes. Here, we introduce a N-terminal peptide enrichment method (Nrich) using a negative selection on filter for the N-terminal peptides with two chemical reagents for labeling free amine and two endoproteases. We identified 6,525 acetylated (or partially acetylated) and 6,570 free protein N-termini from 5,727 proteins. The protein N-termini can be classified into nine groups, such as initial methionine removed or retained, non-terminal residue, signal/transit/pro-peptide removal, putative alternative translational initiation site (methionine removed or retained) and unknown processing, suggesting various proteoform in vivo. In addition, novel protein N-termini was identified in 5`-UTR sequence with pseudo start codon using customized database. Nrich can obtain information about protein stability, localization and function through the observation of finished N-terminal sequence of mature protein.

2017-08-17 | PXD005583 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data