1. ABOUT THE DATASET ------------ Title: Dataset to support improved peptide and protein database search scores in chimeric MS/MS spectra Creator(s): Lily R. Adair (https://orcid.org/0009-0001-2652-9960), Rainer Cramer (https://orcid.org/0000-0002-8037-2511) Organisation(s): University of Reading Rights-holder(s): University of Reading Publication Year: 2023 Description: This dataset contains raw and processed data for liquid atmospheric-pressure matrix-assisted laser desorption/ionisation (LAP-MALDI) mass spectrometry analysis of mixtures of peptides and proteins using a modified Synapt G2-Si with an in-house built atmospheric pressure MALDI source. Chimeric MS/MS peak lists and filtered peak lists produced through the presented data acquisition/analysis workflow were searched using MASCOT. Cite as: Adair, Cramer (2023): Dataset to support improved peptide and protein database search scores in chimeric MS/MS spectra. University of Reading. Dataset. https://doi.org/10.17864/1947.000476 Related publication: Adair, L. R. and Cramer, R. Utilising precursor ion connectivity of different isolation windows to improve peptide and protein identification in chimeric MS/MS spectra. Analytical Chemistry 2023. Submitted. 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: We kindly thank Patrick Emery, Matrix Science Ltd., for developing the processing script utilised in the workflow as well as Waters Corporation for data acquisition and data processing advice. 2. TERMS OF USE ------------ Copyright 2023 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: PhD Project entitled 'Advancing LAP-MALDI mass spectrometry profiling/biotyping for the analysis of microbes and their pathogenicity' Dates: 2022-2025 Funding organisation: University of Reading, Engineering and Physical Sciences Research Council Grant no.:EP/V047485/1 4. CONTENTS ------------ File listing: Peptide_Mixture.zip Protein_Mixture.zip E_Coli_Mixture.zip Each file contains 3 individual folders: including one for the raw data files for each MS and MSMS acquisition, one containing the peak lists used for each MASCOT database search and one containing the MASCOT database search results. Raw files are in a proprietary format which can be opened with the mass spectrometry vendor's software (MassLynx 4.2 by Waters). All data files contain a _extern file with relevant instrument settings recorded. These can be opened in Notepad or a similar text editor. SCL files contain calibration information. Peak lists (as m/z and intensity) are saved as .txt or merged.mgf files which can be opened in Notepad or similar text editor. MASCOT search results are saved in PDF format. 5. METHODS ----------- The dataset contains data that was generated using a commercial mass spectrometer, a Synapt G2-Si HDMS (Waters) equipped with an in-house built AP-MALDI ion source. Masslynx (ver. 4.2; Waters) software was used to collect and process the data. Further processing was carried out using (ver. 2.8.3; Matrix Science) MASCOT Distiller. Peak lists exported from MASCOT Distiller were submitted to a simple script (provided by Matrix Science) for peak list filtering and merging. The filtered and merged peak lists were then submitted for an MS/MS ion search of MASCOT (ver. 2.7; Matrix Science) against the Swissprot database (version 2021_01; 564277 sequences; 203340877 residues).