Raw files description in attached Samples_description.csv

Instrumental Setup

Abbreviation definitions and MS experiment notes:

MPDS: MassPREP™ Protein Digestion Standard (Waters; PN: 186002866-1)

E.Coli: MassPREP™ E.coli Digestion Standard (Waters; PN: 186003196-1)

HD-DDA: "high definition data dependent acquisition"; tandem mass spectrometry couples to precursor ion mobility (transfer cell fragmentation) or fragment ion mobility (trap cell fragmentation)

WbE: "wide band enhancement"; the HD-DDA (Trap) samples were acquired with an improved TOF duty cycle achieved by synchronizing fragment ion ion mobility to orthogonal pusher and TOF mass analyzer; implemented as described by Helm et al. (DOI: 10.1074/mcp.M114.041038)

MS^E: data independent acquisition mass spectrometry method using all-ion-fragmentation with alternating low and high collision energies

HDMS^E: "high definition MS^E"; MS^E coupled to travelling wave ion mobility spectrometry with a focus on precursor ion mobility separation and alignment of corresponding fragment ions to precursor's arrival time distribution

UDMS^E: "ultra definition MS^E"; HDMS^E with drift time-specific collision energies; implemented similarly as described by Distler et al. (DOI: 10.1038/nmeth.2767) following Waters "look-up tables" generation SOP procedure

seMS^E: "signal enhancement MS^E"; MS^E coupled to travelling wave ion mobility spectrometry with a focus on fragment ion mobility spectrometry applying the improved TOF duty cycle achieved by synchronizing fragment ion ion mobility to orthogonal pusher and TOF mass analyzer used previously in the HD-DDA (Trap) + WbE methods