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

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 quantification of histone peptides based on liquid chromatography–tandem
mass spectrometry (LC–MS/MS) analysis. EpiProfile 2.0 is now
optimized for data-independent acquisition through the use of precursor
and fragment extracted ion chromatography to accurately determine
the chromatographic profile and to discriminate isobaric forms of
peptides. The software uses an intelligent retention time prediction
trained on the analyzed samples to enable accurate peak detection.
EpiProfile 2.0 supports label-free and isotopic labeling, different
organisms, known sequence mutations in diseases, different derivatization
strategies, and unusual PTMs (such as acyl-derived modifications).
In summary, EpiProfile 2.0 is a universal and accurate platform for
the quantification of histone marks via LC–MS/MS. Being the
first software of its kind, we anticipate that EpiProfile 2.0 will
play a fundamental role in epigenetic studies relevant to biology
and translational medicine. EpiProfile is freely available at https://github.com/zfyuan/EpiProfile2.0_Family.