iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm

Top-down
proteomics using liquid chromatogram coupled with mass
spectrometry has been increasingly applied for analyzing intact proteins
to study genetic variation, alternative splicing, and post-translational
modifications (PTMs) of the proteins (proteoforms). However, only
a few tools have been developed for charge state deconvolution, monoisotopic/average
molecular weight determination and quantitation of proteoforms from
LC-MS1 spectra. Though Decon2LS and MASH Suite Pro have
been available to provide intraspectrum charge state deconvolution
and quantitation, manual processing is still required to quantify
proteoforms across multiple MS1 spectra. An automated tool
for interspectrum quantitation is a pressing need. Thus, in this paper,
we present a user-friendly tool, called iTop-Q (intelligent Top-down
Proteomics Quantitation), that automatically performs large-scale
proteoform quantitation based on interspectrum abundance in top-down
proteomics. Instead of utilizing single spectrum for proteoform quantitation,
iTop-Q constructs extracted ion chromatograms (XICs) of possible proteoform
peaks across adjacent MS1 spectra to calculate abundances
for accurate quantitation. Notably, iTop-Q is implemented with a newly
proposed algorithm, called DYAMOND, using dynamic programming for
charge state deconvolution. In addition, iTop-Q performs proteoform
alignment to support quantitation analysis across replicates/samples.
The performance evaluations on an in-house standard data set and a
public large-scale yeast lysate data set show that iTop-Q achieves
highly accurate quantitation, more consistent quantitation than using
intraspectrum quantitation. Furthermore, the DYAMOND algorithm is
suitable for high charge state deconvolution and can distinguish shared
peaks in coeluting proteoforms. iTop-Q is publicly available for download
at http://ms.iis.sinica.edu.tw/COmics/Software_iTop-Q.