Combine and conquer: Surfactants, solvents, and chaotropes for robust mass spectrometry based analyses of membrane proteins

Matthew Waas, Subarna Bhattacharya, Sandra Chuppa, Xiaogang Wu, Davin R. Jensen, Ulrich Omasits, Bernd Wollscheid, Brian F. Volkman, Kathleen R. Noon, Rebekah L. Gundry

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

Mass spectrometry (MS) based proteomic technologies enable the identification and quantification of membrane proteins as well as their post-translational modifications. A prerequisite for their quantitative and reliable MS-based bottom-up analysis is the efficient digestion into peptides by proteases, though digestion of membrane proteins is typically challenging due to their inherent properties such as hydrophobicity. Here, we investigated the effect of eight commercially available MS-compatible surfactants, two organic solvents, and two chaotropes on the enzymatic digestion efficiency of membrane protein-enriched complex mixtures in a multiphase study using a gelfree approach. Multiple parameters, including the number of peptides and proteins identified, total protein sequence coverage, and digestion specificity were used to evaluate transmembrane protein digestion performance. A new open-source software tool was developed to allow for the specific assessment of transmembrane domain sequence coverage. Results demonstrate that while Progenta anionic surfactants outperform other surfactants when tested alone, combinations of guanidine and acetonitrile improve performance of all surfactants to near similar levels as well as enhance trypsin specificity to >90%, which has critical implications for future quantitative and qualitative proteomic studies.

Original languageEnglish (US)
Pages (from-to)1551-1559
Number of pages9
JournalAnalytical chemistry
Volume86
Issue number3
DOIs
StatePublished - Feb 4 2014

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Surface-Active Agents
Mass spectrometry
Membrane Proteins
Peptides
Proteins
Anionic surfactants
Guanidine
Hydrophobicity
Complex Mixtures
Organic solvents
Trypsin
Peptide Hydrolases
Proteomics
Open source software
acetonitrile

ASJC Scopus subject areas

  • Analytical Chemistry

Cite this

Combine and conquer : Surfactants, solvents, and chaotropes for robust mass spectrometry based analyses of membrane proteins. / Waas, Matthew; Bhattacharya, Subarna; Chuppa, Sandra; Wu, Xiaogang; Jensen, Davin R.; Omasits, Ulrich; Wollscheid, Bernd; Volkman, Brian F.; Noon, Kathleen R.; Gundry, Rebekah L.

In: Analytical chemistry, Vol. 86, No. 3, 04.02.2014, p. 1551-1559.

Research output: Contribution to journalArticle

Waas, M, Bhattacharya, S, Chuppa, S, Wu, X, Jensen, DR, Omasits, U, Wollscheid, B, Volkman, BF, Noon, KR & Gundry, RL 2014, 'Combine and conquer: Surfactants, solvents, and chaotropes for robust mass spectrometry based analyses of membrane proteins', Analytical chemistry, vol. 86, no. 3, pp. 1551-1559. https://doi.org/10.1021/ac403185a
Waas, Matthew ; Bhattacharya, Subarna ; Chuppa, Sandra ; Wu, Xiaogang ; Jensen, Davin R. ; Omasits, Ulrich ; Wollscheid, Bernd ; Volkman, Brian F. ; Noon, Kathleen R. ; Gundry, Rebekah L. / Combine and conquer : Surfactants, solvents, and chaotropes for robust mass spectrometry based analyses of membrane proteins. In: Analytical chemistry. 2014 ; Vol. 86, No. 3. pp. 1551-1559.
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