TopFD: A Proteoform Feature Detection Tool for Top-Down Proteomics

Overview

Journal Anal Chem

Specialty Chemistry

Date 2023 May 17

PMID 37196155

Authors

Abdul Rehman Basharat

Yong Zang

Liangliang Sun

Xiaowen Liu

Affiliations

Soon will be listed here.

Abstract

Top-down liquid chromatography-mass spectrometry (LC-MS) analyzes intact proteoforms and generates mass spectra containing peaks of proteoforms with various isotopic compositions, charge states, and retention times. An essential step in top-down MS data analysis is proteoform feature detection, which aims to group these peaks into peak sets (features), each containing all peaks of a proteoform. Accurate protein feature detection enhances the accuracy in MS-based proteoform identification and quantification. Here, we present TopFD, a software tool for top-down MS feature detection that integrates algorithms for proteoform feature detection, feature boundary refinement, and machine learning models for proteoform feature evaluation. We performed extensive benchmarking of TopFD, ProMex, FlashDeconv, and Xtract using seven top-down MS data sets and demonstrated that TopFD outperforms other tools in feature accuracy, reproducibility, and feature abundance reproducibility.

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