Linear and differential ion mobility separations of middle-down proteoforms

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Authors
Garabedian, Alyssa
Baird, Matthew A.
Porter, Jacob
Fouque, Kevin Jeanne Dit
Shliaha, Pavel V.
Jensen, Ole N.
Williams, Todd D.
Fernandez-Lima, Francisco
Shvartsburg, Alexandre A.
Issue Date
2018
Type
Article
Language
en_US
Keywords
Electron-transfer dissociation , Tandem mass-spectrometry , Embryonic stem-cells , Gas-phase separations , Posttranslational modifications , Histone tails , Peptide , Protein , Resolution , MS
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Abstract

Comprehensive characterization of proteomes comprising the same proteins with distinct post-translational modifications (PTMs) is a staggering challenge. Many such proteoforms are isomers (localization variants) that require separation followed by top-down or middle-down mass spectrometric analyses, but condensed-phase separations are ineffective in those size ranges. The variants for "middle-down" peptides were resolved by differential ion mobility spectrometry (FAIMS), relying on the mobility increment at high electric fields, but not previously by linear IMS on the basis of absolute mobility. We now use complete histone tails with diverse PTMs on alternative sites to demonstrate that high resolution linear IMS, here trapped IMS (TIMS), broadly resolves the variants of 50 residues in full or into binary mixtures quantifiable by tandem MS, largely thanks to orthogonal separations across charge states. Separations using traveling-wave (TWIMS) and/or involving various time scales and electrospray ionization source conditions are similar (with lower resolution for TWIMS), showing the transferability of results across linear IMS instruments. The linear IMS and FAIMS dimensions are substantially orthogonal, suggesting FAIMS/IMS/MS as a powerful platform for proteoform analyses.

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Alyssa Garabedian, Matthew A. Baird, Jacob Porter, Kevin Jeanne Dit Fouque, Pavel V. Shliaha, Ole N. Jensen, Todd D. Williams, Francisco Fernandez-Lima, and Alexandre A. Shvartsburg. Linear and Differential Ion Mobility Separations of Middle-Down Proteoforms. Analytical Chemistry, 2018 90 (4), 2918-2925
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American Chemical Society
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ISSN
0003-2700
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