1. PROJECT
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Title: Development of liquid AP-MALDI mass spectrometry for microbial profiling and clinical biotyping
Dates: September 2018-August 2019
Funding organisation: EPSRC / University of Reading
Grant no.: EP/R513301/1

2. DATASET
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Title: Dataset to support lipid profiling of bacteria using liquid AP-MALDI MS
Description: This dataset supports the article "Bacterial identification by lipid profiling using liquid atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry". This paper has been submitted in August 2019.  
Publication Year: 2019

Creator(s): Sophie E. Lellman and Rainer Cramer
Organisation(s): University of Reading

3. TERMS OF USE
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This dataset is licensed by the rights-holder(s) under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/.

4. CONTENTS
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File listing:

MS_Lipid_Profile_Bacteria.zip
AMX_PCA_Project_and_Report.zip
Supporting_Files.zip

All data was collected using MassLynx v4.1 (Waters) software. Raw files are filed according to species within the MS_Lipid_Profile_Bacteria.zip folder in the following structure:-
C. jejuni
E. coli
E. faecalis
E. hirae
K. pneumoniae
L. brevis
P. aeruginosa
S. aureus
S. epidermidis
S. pyogenes

Data within the folder named 'Supporting_Files.zip' includes raw files for MS/MS spectra and comparison of solid and liquid MALDI samples. 

All data was obtained using the proprietary software MassLynx 4.1 (Waters) and stored using closed source proprietary data format (Waters .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 .pdf files. 

5. METHOD and PROCESSING
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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 v4.1 (Waters) software was used to collect the data and for data processing. All data files are filed according to species, with nine replicates for each species. Within each individual file, there is a _HEADER and _extern .txt files which contains instrument settings. 
AMX Model Builder (Waters) software was used to perform principle component analysis of the dataset. 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.