Get access

LFQuant: A label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data

Authors

  • Wei Zhang,

    1. Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan, P. R. China
    2. State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China
    Search for more papers by this author
    • These authors contributed equally to the paper.

  • Jiyang Zhang,

    1. Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan, P. R. China
    Search for more papers by this author
    • These authors contributed equally to the paper.

  • Changming Xu,

    1. Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan, P. R. China
    Search for more papers by this author
  • Ning Li,

    1. State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China
    Search for more papers by this author
  • Hui Liu,

    1. Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan, P. R. China
    Search for more papers by this author
  • Jie Ma,

    1. State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China
    Search for more papers by this author
  • Yunping Zhu,

    Corresponding author
    • State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China
    Search for more papers by this author
  • and Hongwei Xie

    Corresponding author
    • Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan, P. R. China
    Search for more papers by this author

  • Colour Online: See the article online to view Fig. 1 in colour.

Correspondence: Hongwei Xie, Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha Hunan 410073, P. R. China

E-mail: xhwei65@nudt.edu.cn

Fax: +86-731-8457337

Additional corresponding author: Yunping Zhu, E-mail: zhuyp@hupo.org.cn

Abstract

Database searching based methods for label-free quantification aim to reconstruct the peptide extracted ion chromatogram based on the identification information, which can limit the search space and thus make the data processing much faster. The random effect of the MS/MS sampling can be remedied by cross-assignment among different runs. Here, we present a new label-free fast quantitative analysis tool, LFQuant, for high-resolution LC-MS/MS proteomics data based on database searching. It is designed to accept raw data in two common formats (mzXML and Thermo RAW), and database search results from mainstream tools (MASCOT, SEQUEST, and X!Tandem), as input data. LFQuant can handle large-scale label-free data with fractionation such as SDS-PAGE and 2D LC. It is easy to use and provides handy user interfaces for data loading, parameter setting, quantitative analysis, and quantitative data visualization. LFQuant was compared with two common quantification software packages, MaxQuant and IDEAL-Q, on the replication data set and the UPS1 standard data set. The results show that LFQuant performs better than them in terms of both precision and accuracy, and consumes significantly less processing time. LFQuant is freely available under the GNU General Public License v3.0 at http://sourceforge.net/projects/lfquant/.

Get access to the full text of this article

Ancillary