TopFD
TopFD (Top-down mass spectral Feature Detection) is a software tool
for top-down spectral deconvolution and a successor to MS-Deconv.
It groups top-down spectral
peaks into isotopic envelopes and converts isotopic envelopes to
monoisotopic neutral masses. In addition, it extracts proteoform features
from LC-MS or CE-MS data. TopFD integrates algorithms for proteoform feature detection,
feature boundary refinement, and machine learning models for evaluating proteoform features.
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Code Availability:
TopFD has been made available as part of TopPIC suite and can be downloaded from
https://github.com/toppic-suite/toppic-suite/.
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Executables, manual, and tutorials:
You can download zipped executable files and find a manual and
tutorials of TopFD at
https://www.toppic.org/.
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Evaluation Scripts:
Evaluation scripts are made available as a GitHub repository and are available at
https://github.com/ARBasharat/TopFD_Evaluation_Scripts.
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Data:
The raw and mzML files as well as processed data of the 5 datasets used in the paper are
available at
here.
The dataset includes (1) raw data files, (2) mzML data files, (3)
Extracted features, (4) training data and machine learning model for
ECScore, and (5) feature list after removing artifacts.