10.1021/acs.analchem.7b03401.s001 Kevin Jeanne Dit Fouque Kevin Jeanne Dit Fouque Alyssa Garabedian Alyssa Garabedian Jacob Porter Jacob Porter Matthew Baird Matthew Baird Xueqin Pang Xueqin Pang Todd D. Williams Todd D. Williams Lingjun Li Lingjun Li Alexandre Shvartsburg Alexandre Shvartsburg Francisco Fernandez-Lima Francisco Fernandez-Lima Fast and Effective Ion Mobility–Mass Spectrometry Separation of d‑Amino-Acid-Containing Peptides American Chemical Society 2017 Separation fragment epimer time-of-flight mass spectrometry DAACP quantification IMS-MS separation TIMS-CID-MS Standard proteomics protocols IMS TWIMS CID peptide ion mobility spectrometry charge state resolution mass spectrometry 2017-10-05 00:00:00 Journal contribution https://acs.figshare.com/articles/journal_contribution/Fast_and_Effective_Ion_Mobility_Mass_Spectrometry_Separation_of_d_Amino-Acid-Containing_Peptides/5517016 Despite often minute concentrations in vivo, d-amino acid containing peptides (DAACPs) are crucial to many life processes. Standard proteomics protocols fail to detect them as d/l substitutions do not affect the peptide parent and fragment masses. The differences in fragment yields are often limited, obstructing the investigations of important but low abundance epimers in isomeric mixtures. Separation of d/l-peptides using ion mobility spectrometry (IMS) was impeded by small collision cross section differences (commonly ∼1%). Here, broad baseline separation of DAACPs with up to ∼30 residues employing trapped IMS with resolving power up to ∼340, followed by time-of-flight mass spectrometry is demonstrated. The d/l-pairs coeluting in one charge state were resolved in another, and epimers merged as protonated species were resolved upon metalation, effectively turning the charge state and cationization mode into extra separation dimensions. Linear quantification down to 0.25% proved the utility of high resolution IMS-MS for real samples with large interisomeric dynamic range. Very close relative mobilities found for DAACP pairs using traveling-wave IMS (TWIMS) with different ion sources and faster IMS separations showed the transferability of results across IMS platforms. Fragmentation of epimers can enhance their identification and further improve detection and quantification limits, and we demonstrate the advantages of online mobility separated collision-induced dissociation (CID) followed by high resolution mass spectrometry (TIMS-CID-MS) for epimer analysis.