Poster Presentation HUPO 2019 - 18th Human Proteome Organization World Congress

Fast and fully automated analysis of HDX-MS data with deMix through robust peptide feature comparison (#742)

Seungjin Na 1 , Jae-Jin Lee 2 , Jong Wha J Joo 3 , Kong-Joo Lee 2 , Eunok Paek 1
  1. Hanyang University, Seoul, SEOUL, South Korea
  2. Ewha Womans University, Seoul, South Korea
  3. Dongguk University-Seoul, Seoul, South Korea

Characterization of protein structural changes in response to protein modifications, ligand or chemical binding, or protein-protein interactions is essential for understanding protein function and its regulation. Hydrogen/Deuterium Exchange (HDX) coupled with mass spectrometry (MS) is one of the most powerful tools for characterizing the protein dynamics and changes of protein conformation. With the advent of high throughput technologies, the data size grows everyday and an automated tool is essential for the analysis. Here, we introduce fully automated software, called deMix (decode deuterated mixture) that performs binomial fitting of deuterium contribution and deals directly with deuterated isotopic distributions. deMix gets robust over noise interfering with deuterated distributions through two procedures 1) dynamically determining the elution time spans for candidate peptide masses and aggregated isotopic distributions of the same peptide feature over elution time and 2) measuring how many peaks are matched in terms of abundance between theoretical and experimental isotopic distributions (referred to as Matched Peaks Count). The proposed method also has strength in analyzing bimodal deuterated distributions, arising from EX1 behavior or heterogeneous peptides in conformational isomer proteins. In an HDX-MS analysis of Nm23-H1, a tumor metastasis suppressor, deMix clearly showed that the HDX rates were increased under an oxidative condition (compared with a native condition). Notably, deMix discovered bimodal deuteration behaviors indicating two conformational states by stepwise oxidation of Nm23-H1. The software is freely available at