Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate
The ionic detergent sodium deoxycholate (SDC) is compatible with in-solution tryptic digestion and LC-MS/MS-based shotgun proteomics by virtue of being easy to separate from the peptide products via precipitation in acidic buffers. However, it remains unclear whether unique human peptides co-precipi...
| Main Authors: | , , , , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2016
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| Online Access: | https://hdl.handle.net/10356/80250 http://hdl.handle.net/10220/40445 |
| _version_ | 1811689506921775104 |
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| author | Serra, Aida Zhu, Hongbin Gallart-Palau, Xavier Park, Jung Eun Ho, Hee Haw Tam, James P. Sze, Siu Kwan |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Serra, Aida Zhu, Hongbin Gallart-Palau, Xavier Park, Jung Eun Ho, Hee Haw Tam, James P. Sze, Siu Kwan |
| author_sort | Serra, Aida |
| collection | NTU |
| description | The ionic detergent sodium deoxycholate (SDC) is compatible with in-solution tryptic digestion and LC-MS/MS-based shotgun proteomics by virtue of being easy to separate from the peptide products via precipitation in acidic buffers. However, it remains unclear whether unique human peptides co-precipitate with SDC during acid treatment of complex biological samples. In this study, we demonstrate for the first time that a large quantity of unique peptides in human blood plasma can be co-precipitated with SDC using an optimized sample preparation method prior to shotgun proteomic analysis. We show that the plasma peptides co-precipitated with SDC can be successfully recovered using a sequential re-solubilization and precipitation procedure, and that this approach is particularly efficient at the extraction of long peptides. Recovery of peptides from the SDC pellet dramatically increased overall proteome coverage (>60 %), thereby improving the identification of low-abundance proteins and enhancing the identification of protein components of membrane-bound organelles. In addition, when we analyzed the physiochemical properties of the co-precipitated peptides, we observed that SDC-based sample preparation improved the identification of mildly hydrophilic/hydrophobic proteins that would otherwise be lost upon discarding the pellet. These data demonstrate that the optimized SDC protocol is superior to sodium dodecyl sulfate (SDS)/urea treatment for identifying plasma biomarkers by shotgun proteomics. |
| first_indexed | 2024-10-01T05:49:12Z |
| format | Journal Article |
| id | ntu-10356/80250 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:49:12Z |
| publishDate | 2016 |
| record_format | dspace |
| spelling | ntu-10356/802502023-02-28T17:00:12Z Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate Serra, Aida Zhu, Hongbin Gallart-Palau, Xavier Park, Jung Eun Ho, Hee Haw Tam, James P. Sze, Siu Kwan School of Biological Sciences Trypsin digestion Plasma proteome Mass spectrometry Shotgun proteomics Sodium deoxycholate The ionic detergent sodium deoxycholate (SDC) is compatible with in-solution tryptic digestion and LC-MS/MS-based shotgun proteomics by virtue of being easy to separate from the peptide products via precipitation in acidic buffers. However, it remains unclear whether unique human peptides co-precipitate with SDC during acid treatment of complex biological samples. In this study, we demonstrate for the first time that a large quantity of unique peptides in human blood plasma can be co-precipitated with SDC using an optimized sample preparation method prior to shotgun proteomic analysis. We show that the plasma peptides co-precipitated with SDC can be successfully recovered using a sequential re-solubilization and precipitation procedure, and that this approach is particularly efficient at the extraction of long peptides. Recovery of peptides from the SDC pellet dramatically increased overall proteome coverage (>60 %), thereby improving the identification of low-abundance proteins and enhancing the identification of protein components of membrane-bound organelles. In addition, when we analyzed the physiochemical properties of the co-precipitated peptides, we observed that SDC-based sample preparation improved the identification of mildly hydrophilic/hydrophobic proteins that would otherwise be lost upon discarding the pellet. These data demonstrate that the optimized SDC protocol is superior to sodium dodecyl sulfate (SDS)/urea treatment for identifying plasma biomarkers by shotgun proteomics. MOE (Min. of Education, S’pore) Accepted version 2016-04-15T06:33:16Z 2019-12-06T13:45:51Z 2016-04-15T06:33:16Z 2019-12-06T13:45:51Z 2016 Journal Article Serra, A., Zhu, H., Gallart-Palau, X., Park, J. E., Ho, H. H., Tam, J. P., et al. (2016). Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate. Analytical and Bioanalytical Chemistry, 408(7), 1963-1973. 1618-2642 https://hdl.handle.net/10356/80250 http://hdl.handle.net/10220/40445 10.1007/s00216-016-9312-7 en Analytical and Bioanalytical Chemistry © 2016 Springer Berlin Heidelberg. This is the author created version of a work that has been peer reviewed and accepted for publication by Analytical and Bioanalytical Chemistry, Springer Berlin Heidelberg. It incorporates referee’s comments but changes resulting from the publishing process, such as copyediting, structural formatting, may not be reflected in this document. The published version is available at: [http://dx.doi.org/10.1007/s00216-016-9312-7]. 31 p. application/pdf |
| spellingShingle | Trypsin digestion Plasma proteome Mass spectrometry Shotgun proteomics Sodium deoxycholate Serra, Aida Zhu, Hongbin Gallart-Palau, Xavier Park, Jung Eun Ho, Hee Haw Tam, James P. Sze, Siu Kwan Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate |
| title | Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate |
| title_full | Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate |
| title_fullStr | Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate |
| title_full_unstemmed | Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate |
| title_short | Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate |
| title_sort | plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate |
| topic | Trypsin digestion Plasma proteome Mass spectrometry Shotgun proteomics Sodium deoxycholate |
| url | https://hdl.handle.net/10356/80250 http://hdl.handle.net/10220/40445 |
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