Native MS dataset for: "High performance interface for boosting ion transmission in native mass spectrometry and beyond"

Mass spectrometry (MS) dataset used in: High performance interface for boosting ion transmission in native mass spectrometry and beyond. Alan Kádek, Ronja Pogan, Thomas Kierspel, Yinfei Lu, Sandeep Mishra, Pierre Chouzenoux, Jan Commandeur, Alexandros Lekkas, Dimitris Papanastasiou, Charlotte Uetrecht. Journal XXX, (YYYY). doi: ZZZ

Used for the characterization and benchmarking of a novel design of ion transfer inerface (ITI) aimed namely at native mass spectrometry and native MS-based ion delivery techniques.

Samples:

Standard protein samples (see table) obtained from Sigma-Aldrich / Merck buffer exchanged into ammonium acetate solution. Human norovirus strain GII.4 Saga virus-like particles (NoVLPs; GenBank: AB447457.1) were prepared by recombinant expression.

Instrument settings:

Samples were electrosprayed from in-house prepared nanoESI emitters pulled from borosilicate glass capillaries (Kwik-Fil 1B120F-4, World Precision Instruments) con-ductively coated on the outside by a 40 nm layer of sputtered gold. Instrument parameters were optimized in a sample-specific manner for maximum ion transmission, while keeping ion activation minimal.

From quadrupole onwards, the base high-mass modified quadrupole / time-of-flight (Q-ToF) Ultima US mass spectrometer (Micromass / MSVision), on which the novel ITI source or the standard source were mounted and side-by-side compared, had identical settings. Namely, the 30,000 m/z quadrupole operating in a broadband transmission mode was kept harmonically sweeping its set mass in a sample-appropriate mass range, collision cell was filled with argon (or xenon for NoVLPs) of 5.0 purity (Linde Gas) and the ToF pusher cycle time was varied based on the sample. Data acquired by a multi-channel plate (MCP) detector were processed by the time-to-digital converter implemented in the instrument (with 1 MHz sampling rate) and were binned directly in the instrument with a bunching factor 4 (20 for NoVLPs).

Data processing:

Raw acquired data deposited here in the Waters proprietary .raw format were first converted to the open .mzML format (also deposited) in ProteoWizard 3.0.23192 and read into Python 3.11.7 using the pyOpenMS 3.4.0 library. A set of custom Python scripts (available together with the raw data) summed data from subsequent scans without any smoothing with the scan ranges defined in the accompanying .txt file and handled further as needed for the analyses described in the pre-print and final publication.