1. PROJECT ------------ Title: Developing liquid AP-MALDI MS as a rapid diagnostics method for bovine tuberculosis Dates: February 2021-March 2023 Funding organisation: EPSRC / University of Reading and DEFRA Grant no.: EP/R513301/1 and 26952 2. DATASET ------------ Title: Dataset to support LAP-MALDI MS profiling and identification of biomarkers for the detection of bovine tuberculosis Description: This dataset contains LAP MALDI MS profile data from 95 cattle nasal swabs, as well as MS/MS data performed in order to identify biomarkers detected in the MS profiles. Subsequent PCA and LDA analysis was performed, whose models are contained within this dataset alongside their respective cross-validation. An in-house built LAP-MALDI MS coupled to a Synapt G2-Si was used for all data acquisitions. All data presented was acquired between February 2022 and December 2022. Publication Year: 2024 Creator(s): Sophie E. Lellman, Rainer Cramer. Organisation(s): University of Reading Rightsholder(s): Crown Cite as: Lellman, Sophie and Cramer, Rainer (2024): Dataset to support LAP-MALDI MS profiling and identification of biomarkers for the detection of bovine tuberculosis. University of Reading. Dataset. https://doi.org/10.17864/1947.000443 Related publication: "LAP-MALDI MS profiling and identification of potential biomarkers for the detection of bovine tuberculosis". Sophie E. Lellman et al., J. Agric. Food Chem. 2023, 71, 13899-13905. 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 Waters Corporation for access to the AMX [Beta] software. We also thank APHA, Crichton Royal Farm and the local farms for collecting and donating samples for this study, as well as DEFRA who provided funding (ref. 26952), continuous support throughout the project and assistance in obtaining bTB animal samples. This work was also supported by EPSRC through grant EP/R513301/1. 3. TERMS OF USE ----------------- Copyright 2024, Crown. This dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/. 4. CONTENTS ------------ File listing: AMX_Models.zip bTB_Fragmentation_Spectra.zip Cross-Validation_Reports.zip MS_Profiles.zip Supporting_Files.zip Data within the 'MS_Profiles' folder includes raw files from all cattle samples which were subjected to a short digestion protocol as detailed in the manuscript as well as six calibration folder with a folder name starting with '20220207_SL_MYOGLOBIN' or '20220207_SL_NAI'. Data within the 'bTB_Fragmentation_Spectra' folder were obtained from selected processed nasal swab samples. All MS data were obtained using the proprietary software MassLynx 4.2 (Waters) and stored using closed source proprietary data format (.raw). Data is stored for full compatibility with Waters proprietary software; however, several free open-source software packages are available to convert the raw data to the open-source file format mzML, e.g. the msconvert utility by the ProteoWizard project http://proteowizard.sourceforge.net/downloads.shtml. Multivariate models were produced using AMX Model Builder (Waters) software. This software is not openly available. The file format is proprietary. Cross-validation reports of the multivariate model are present as .html files. Data within the 'Supporting_Files' folder includes metadata for all animals sampled from and SOPs for sample collection and processing. 5. METHOD and PROCESSING -------------------------- The dataset contains data that was acquired on a commercial mass spectrometer, a Synapt G2-Si (Waters), coupled to an in-house built atmospheric pressure MALDI ion source. MassLynx v4.2 (Waters) software was used to collect the data and for data processing. All MS profile data from nasal swabs obtained from cattle are present in one folder. Within each individual folder, there are a _HEADER and _extern .txt files which contain instrument settings. All MS/MS fragmentation data is present within the same folder. Within each individual folder, there are a _HEADER and _extern .txt files which contain instrument settings. AMX Model Builder (Waters) software was used to perform principle component analysis of the MS profiles. The multivariate model can be viewed using AMX software. Cross-validation of the multivariate model was performed leaving 20% of the data out and testing this against the model to determine accuracy and specificity. Driftscope (Waters) software was used to selectively filter for MS/MS spectra multiply charged ions, whose spectra were subsequently deconvoluted using MaxEnt (Waters) software.