1. ABOUT THE DATASET ------------ Title: Dataset to support 'Liquid atmospheric pressure matrix-assisted laser desorption/ionization (LAP-MALDI) mass spectrometry using a commercial ion source and Orbitrap mass analyzer' Creator(s): Bob Challen, Lily R. Adair, Rainer Cramer Organisation(s): University of Reading Rights-holder(s): University of Reading Publication Year: 2024 Description: The application of liquid atmospheric-pressure matrix-assisted laser desorption/ionisation (LAP-MALDI) in conjunction with a commercial AP-MALDI ion source coupled to an Orbitrap mass analyser was investigated. This dataset contains raw data files, including AP-MALDI-Orbitrap, LAP-MALDI-Orbitrap and LAP-MALDI-QTOF data of an 8-peptide mixture, a 3-protein mixture, and a bacterial extract. Cite as: Challen, Adair, Cramer (2024): Dataset to support 'Liquid atmospheric pressure matrix-assisted laser desorption/ionization (LAP-MALDI) mass spectrometry using a commercial ion source and Orbitrap mass analyzer'. University of Reading. Dataset. https://doi.org/10.17864/1947.001326 Related publication: Challen, B., Adair, L.R. and Cramer, R. (2024). Liquid atmospheric pressure matrix-assisted laser desorption/ionization (LAP-MALDI) mass spectrometry using a commercial ion source and Orbitrap mass analyzer. Analytical Chemistry, 96 (40). pp. 15865-15870. https://doi.org/10.1021/acs.analchem.4c04458 Contact: Prof. Rainer Cramer, Department of Chemistry, University of Reading, Reading RG6 6DX, United Kingdom, Tel: 0118 378 4550, Email: r.k.cramer@reading.ac.uk. Acknowledgements: This research was supported by the Engineering and Physical Sciences Research Council (EPSRC) through grant EP/V047485/1. We thank S. Kennerley (KR Analytical), G. Frache (Luxembourg Institute of Science and Technology) and K. Strupat (Thermo Fisher Scientific) for help with sourcing and installing the AP-MALDI source, and the Chemical Analysis Facility at the University of Reading for providing access to the Orbitrap. 2. TERMS OF USE ------------ Copyright 2024 University of Reading. This dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/. 3. PROJECT AND FUNDING INFORMATION ------------ Title: A Cost-Effective High-Speed Clinical Diagnostics Instrument for Large Population Screening Based on Novel Liquid AP-MALDI MS Technology Dates: 10/2021-09/2025 Funding organisation: Engineering and Physical Sciences Research Council Grant no.: EP/V047485/1 4. CONTENTS ------------ File listing: -Figure_1.7z ---.mzml Files ---.Raw Files -Figure_2.7z ---.mzml Files ---.Raw Files -Basic-mzml-plotter_1-1-1.7z The file contents contain data for their respective figures. Figure_1.7z contains a folder with .raw datafiles, and a folder with .mzml files converted from the .raw files using the msconvert program. The .mzml files were used to analyse all data and generate all figures. Each file has the respective figure name at the beginning of the filename. 1a includes conventional solid AP-MALDI data for an 8-peptide mixture. 1b-1d includes 3 acquisitions of the same 8-peptide mixture via LAP-MALDI taken consecutively, first on an Orbitrap, then on a Q-TOF, and finally again on the Orbitrap instrument. 1i-j contain an MS/MS acquisition on the Orbitrap of a triply charged angiotensin I peak from within the 8-peptide mixture at 50 fmol spotted on target. 1k includes a 5-uM mixture of cyctochrome C, myoglobin and ubiquitin analysed on the Orbitrap. Figure_2.7z also contains a folder with .raw datafiles, and a folder with .mzml files converted from the .raw files using the msconvert program. The .mzml files were used in all analysis and figure production. Each file has the respective figure name at the beginning of the filename. 2a includes a LAP-MALDI-Orbitrap acquisition of the 8-peptide mixture over several minutes. 2b_1 and 2b_2 contain an conventional solid AP-MALDI-Orbitrap analysis of the 8-peptide mixture prepared via a dried-droplet sample preparation, with no laser beam movement in 2b_1 and spiral laser beam movement in 2b_2. 2c and 2d contain MS and MS/MS acquisitions of a K. pneumoniae sample, with 2c showing the full MS profile, and 2d showing the MS/MS fragmentation of the m/z 1194 peak. The MS/MS acquisition files for the 2 other charge states of the same protein are also included. Basic-mzml-plotter-1.1.1.zip contains the necessary python files to run the application used for the data visualisation and a portion of the data processing for the included mzml datafiles, and also includes a README file detailing installation and usage instructions. 5. METHODS ----------- The dataset primarily contains data acquired on a LTQ Orbitrap XL (Thermo Fisher Scientific; Bremen, Germany) equipped with an AP/MALDI (ng) UHR (MassTech; Columbia, MD, USA) ion source. The data acquired for figure 2c was acquired on a Synapt G2-Si (Waters; Wilmslow, UK) equipped with an in-house built LAP-MALDI ion source. To allow for the alignment of processing methods between the two instruments, all data files were converted into .mzml format and viewed via a custom python script. This script can be found free of charge both within this repository, and at the following GitHub link: https://github.com/BobChallen/Basic-mzml-plotter The deconvoluted inset of the three protein mixture in figure 1k was produced with Unidec version 4.4.1, available free of charge at the following GitHub link: https://github.com/michaelmarty/UniDec