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/releases/tag/v1.6_beta.
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Executables:
You can download the zipped executable files using
for Windows and
for Linux/MAC .
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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 data files have been made available for all 5 data sets used in the study and can be accessed using
RAW
and mzML files.
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Extracted Feature:
Proteoform features extrated from all data sets using TopFD, ProMex, FlashDeconv and Xtract have been made available at
link.
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Training Data and Model file:
Data used to train ECScore model and the trained model are available at
link.
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Processed Feature List:
Proteoform features following the removal of mass artifacts are available at
link.