EpiProfile statistics

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Citations per year

Number of citations per year for the bioinformatics software tool EpiProfile
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Tool usage distribution map

This map represents all the scientific publications referring to EpiProfile per scientific context
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Protocols

EpiProfile specifications

Information


Unique identifier OMICS_31505
Name EpiProfile
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Programming languages MATLAB
License GNU General Public License version 3.0
Computer skills Medium
Version 2.0
Stability Stable
Requirements
Xcalibur
Maintained Yes

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Documentation


Maintainer


  • person_outline Benjamin Garcia

Publications for EpiProfile

EpiProfile citations

 (13)
call_split

Characterization of histone acylations links chromatin modifications with metabolism

2017
Nat Commun
PMCID: 5656686
PMID: 29070843
DOI: 10.1038/s41467-017-01384-9
call_split See protocol

[…] performed with an AGC target of 3 × 104 using an injection time limit of 30 or 60 ms. All acquisitions were performed in positive mode polarity.Data analysis was performed using our in-house software EpiProfile with a 10-ppm tolerance for extracting peak areas from raw files. The relative abundances of acyl-PTMs were calculated by dividing the intensity the modified peptide by the sum of all modif […]

library_books

Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b

2017
PMCID: 5506665
PMID: 28701172
DOI: 10.1186/s13072-017-0143-3

[…] Orbitrap was operated in data-dependent mode essentially as previously described []. Relative abundances of peptide species were calculated by chromatographic peak integration of full MS scans using EpiProfile []. Where necessary, peptide and PTM identity were verified by manual inspection of MS/MS spectra. […]

library_books

Metabolic labeling in middle down proteomics allows for investigation of the dynamics of the histone code

2017
PMCID: 5501349
PMID: 28683815
DOI: 10.1186/s13072-017-0139-z

[…]  0.86; Additional file: Table S1), and the significance of the correlation was assessed using the t test (p value of the avg correlation = 0.027). Peptides were quantified using our in-house software EpiProfile []. After assessing efficient labeling, we used the EMT model to analyze and compare old (unlabeled) versus newly synthesized (heavy KR labeled) histones during mesenchymal transition. To d […]

call_split

Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription

2017
Nature
PMCID: 5576860
PMID: 28682306
DOI: 10.1038/nature23267
call_split See protocol

[…] entroid mode in the ion trap with sequential isolation windows of 50 m/z with an AGC target of 3×104, a CID collision energy of 35 and a maximum injection time of 50 msec. The data was searched using EpiProfile with Schizosaccharomyces pombe database. The peptide relative ratio was calculated using the total area under the extracted ion chromatograms of all peptides with the same amino acid sequen […]

call_split

Quantitative chromatin proteomics reveals a dynamic histone post translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites

2017
Sci Rep
PMCID: 5428830
PMID: 28377601
DOI: 10.1038/s41598-017-00687-7
call_split See protocol

[…] difications: methyl (+propionyl), dimethyl, trimethyl, acetyl, and propionyl (K). Peptides were filtered for high confidence (FDR < 1%) using Fixed Value validator. Quantification was performed using EpiProfile, which performs extracted ion chromatography of selected peptides. Once the peak area was extracted, the relative abundance of a given PTM was calculated by dividing its intensity by the su […]

library_books

Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells

2017
Sci Rep
PMCID: 5209743
PMID: 28051095
DOI: 10.1038/srep39406

[…] d in the ion trap. The relative abundance of each modification, expressed as a percentage on a histone peptide sequence, was quantified by analyzing its MS and MS/MS spectra via an in-house software, EpiProfile. […]


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EpiProfile institution(s)
Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA, USA
EpiProfile funding source(s)
Supported by NIH grants GM110174, AI118891, and CA196539; DOD grant W81XWH-113-1-0426; an UPenn Epigenetics Institute pilot grant and NIH grants TL1TR001880 and T32GM008275.

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