Introduction

Advances in proteomics research involve the use of high-precision and high-resolution mass spectrometry instruments. Although hardware improvements are the main impetus for the acquisition of high-quality data, enhancements in software tools are also needed. In this study, recalibration was verified as an important way to improve data accuracy. A new version tool, known as FTDR 2.0, was developed to recalibrate the mass-to-charge ratio error of most observed parent ions to the sub part per million level in routine experiments. First, many new parameters were introduced and screened as features online to reduce systematic error and to adapt to various data sets. Second, a support vector regression model was trained to characterize the complex nonlinear maps from features to mass-to-charge ratio measurement errors. Third, a specific mass-to-charge ratio error tolerance for each parent ion was estimated by considering the impact of signal intensity. FTDR 2.0 is a user-friendly tool that supports most commonly used data standards and formats. A C++ library and the source code are provided to support the redevelopment and integration into other mass spectrometry data processing tools. The performance of FTDR 2.0 was verified using several experimental data sets from different research programs. Recalibration with FTDR 2.0 has been proved to improve the peptide identification in qualitative, quantitative, and post-translational modification analyses.

Publications

  1. FTDR 2.0: a tool to achieve sub-ppm level recalibrated accuracy in routine LC-MS analysis.
    Cite this
    Zhang J, Ma J, Zhang W, Xu C, Zhu Y, Xie H, 2013-09-01 - Journal of proteome research

Credits

  1. Jiyang Zhang
    Developer

    College of Mechatronic Engineering and Automatic Control, National University of Defense Technology, China

  2. Jie Ma
    Developer

  3. Wei Zhang
    Developer

  4. Changming Xu
    Developer

  5. Yunping Zhu
    Developer

  6. Hongwei Xie
    Investigator

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Summary
AccessionBT000280
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByHongwei Xie