0. SECTIONS ------------- 1. Project 2. Dataset 3. Terms of Use 4. Contents 5. Method and Processing 1. PROJECT ------------ Title: Developing liquid AP-MALDI MS as a rapid large-scale classification method for determining farm animal health Dates: January 2018/December 2020 Funding organisation: Biotechnology and Biological Sciences Research Council Grant no.: BB/R002975/1 2. DATASET ------------ Title: Liquid Atmospheric Pressure MALDI MS for high-throughput diagnosis and antibiotic resistance detection Description: AP-MALDI MS profiling coupled with multivariate analysis for the detection of farm-related diseases using a simple one-pot sample preparation of milk. Milk samples were collected at the Centre for Dairy Research (CEDAR) of University of Reading (UK). The analysis performed on the test set allowed the detection of clinical mastitis with a correct classification rate of 98.57% and the correct detection of mastitis 2 days before the clinical event with a sensitivity of 70% and a specificity of 100%. Publication Year: 2021 Creator(s): Cristian Piras, and Rainer Cramer 3. TERMS OF USE ----------------- Copyright 2021 University of Reading. This dataset is licensed by the rights-holder under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/. 4. CONTENTS ------------ File listing: - Clinical_mastitis.zip Description: The file contains the raw data, the Abstract Model Builder (Waters), the jmpSAS multivariate project and the Excel matrix. The Excel matrix and the multivariate AMX model retention times map the Clinical mastitis samples on the chromatogram. - Preclinical_mastitis_Jul_Aug.zip Description: The file contains the raw data, the Abstract Model Builder (Waters) multivariate project, the jmpSAS multivariate project and the Excel matrix. The Excel matrix ("Preclinical mastitis.xls") and the multivariate AMX model ("Preclinical mastitis.amx") retention times map the Pre-clinical mastitis samples on the chromatogram. - Preclinical_mastitis_Sep_Oct.zip Description: The file contains the raw data. The Excel matrix ("Preclinical mastitis.xls") and the multivariate AMX model ("Preclinical mastitis.amx") present in the "Preclinical_mastitis_Jul_Aug.zip" file map the Pre-clinical mastitis samples on the chromatogram. - Preclinical_mastitis_Nov_Dec.zip Description: The file contains the raw data. The Excel matrix ("Preclinical mastitis.xls") and the multivariate AMX model ("Preclinical mastitis.amx") present in the "Preclinical_mastitis_Jul_Aug.zip" file map the Pre-clinical mastitis samples on the chromatogram. - Ampicillin_resistance.zip Description: The file contains the raw data, the Abstract Model Builder (Waters) multivariate project and the Excel matrix. The Excel matrix and the multivariate AMX model retention times map the beta-lactamase curve and the analysed samples on the chromatogram. - Preclinical_mastitis_data.xlsx Description: The file contains the excel matrix including all the information about pre-clinical experiments. It contains the spectral information and all the metadata for each sample analysed. All data was obtained using proprietary software MassLynx (Waters) and stored using closed source proprietary data format (Waters .raw). Data is stored as is to maintain full compatibility with Waters proprietary software; however several free open source software packages are available to convert the data to an open source file format mzML, e.g. msconvert utility by ProteoWizard project http://proteowizard.sourceforge.net/downloads.shtml. Multivariate models were produced with AMX, beta-version software developed by Waters. It is not openly available. The file format is proprietary. 5. METHOD and PROCESSING -------------------------- The dataset contains data that was generated using a commercial mass spectrometer Synapt-G2Si HDMS (Waters) equipped with an in-house developed AP-MALDI ion source. Masslynx (ver. 4.2; Waters) software was used to collect and process the data. Further processing making use of the ion mobility function was performed with DriftScope (v.2.8; Waters) as necessary (e.g. charge state filtering, drift time export). All data files contain a _HEADER and _extern file with relevant instrument settings and employed methods recorded. These can be opened in Notepad or a similar text editor.