Research ArticleCELL BIOLOGY

Evidence that the ProPerDP method is inadequate for protein persulfidation detection due to lack of specificity

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Science Advances  14 Aug 2020:
Vol. 6, no. 33, eabb6477
DOI: 10.1126/sciadv.abb6477
  • Fig. 1 A schematic presentation of the ProPerDP method.

    Workflow 1 was from (10) and was used to separate the IAB-labeled proteins. Workflow 2 was used to separate IAB-labeled peptides.

  • Fig. 2 Using the ProPerDP method to analyze protein samples from E. coli strains.

    (A) Detected persulfidation levels of proteome samples from ΔoxyR and wt strains. (B) Distribution of the identified protein species in these two proteome samples. (C) Numbers of proteins and peptides detected by LC-MS/MS.

  • Fig. 3 Using LC-MS/MS to analyze Rdl2, OxyR4C→A, and psGFP 1.1.

    We used the Protein Digestor tool of http://db.systemsbiology.net to perform the in silico digestion, and results showed that after trypsin digestion, Rdl2 can release 4.5%, OxyR4C→A can release 6.9%, and psGFP 1.1 can release 11.5% of Cys-containing peptides (theoretical, green bars). When using LC-MS to analyze the digested proteins, we experimentally detected 2.6, 12.5, and 13.4% of Cys-containing peptides, respectively (detected, orange bars). The percentage was calculated from the signal intensity of the peptide precursor.

  • Fig. 4 The distribution of proteins detected from three parallel samples using workflow 1.

    Protein numbers are shown in Table 2.

  • Table 1 LC-MS/MS analysis of peptides detected from E. coli and yeast samples using workflow 2.

    SamplePeptide
    number
    Cys-containing
    peptide
    number
    Percentage
    OxyR15500%
    wt13021.54%
    MG1655a5123.92%
    MG1655b5811.72%
    MG1655c4449.09%
    BY474217284.65%
  • Table 2 LC-MS/MS analysis of proteins obtained from three parallel samples using workflow 1.

    SampleProtein
    number
    Peptide
    number
    Cys-containing
    peptide
    number
    1361125916
    22439409
    328083540

Supplementary Materials

  • Supplementary Materials

    Evidence that the ProPerDP method is inadequate for protein persulfidation detection due to lack of specificity

    Kaili Fan, Zhigang Chen, Huaiwei Liu

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    • Legends for data files S1 to S3

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