MALDI mass spectra of Escherichia coli WDCM 00090 ATCC® 11775™ and Shigella flexneri ATCC® 12022™ protein and lipid extracts and also classification results
This readme file was generated on 2023-07-27 by Adrian Arendowski
GENERAL INFORMATION
Title of Dataset: MALDI MS spectra of Escherichia coli and Shigella flexneri protein and lipid extracts
Author/Principal Investigator Information
Name: Adrian Arendowski
ORCID: 0000-0002-8496-6800
Institution: Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University
Address: Wileńska 4 Str, Toruń, 87-100, Poland
Email: aarendowski@umk.pl
Date of data collection: from 2023-07-03 to 2023-07-27
Geographic location of data collection: Poland
Keywords: Escherichia coli; identification; MALDI; mass spectrometry; microorganisms; Shigella flexneri; proteins; lipids
Language information: English
Information about funding sources that supported the collection of the data: National Science Center Poland, grant MINIATURA 6; 2022/06/X/NZ6/00226
SHARING/ACCESS INFORMATION
Licenses/restrictions placed on the data: CC BY-SA
DATA & FILE OVERVIEW
File List:
1. Lipid profile MALDI MS Bruker files.zip (Folder contains MALDI MS spectral files of lipid extracts from Escherichia coli ATCC® 11775™ and Shigella flexneri ATCC® 12022™ generated by Bruker ultrafleXtreme MALDI mass spectrometer readable in Bruker FlexAnalysis software)
2. Lipid profile MALDI MS peak lists.zip (Folder contains files with a list of signals from spectra of lipid extracts from Escherichia coli ATCC® 11775™ and Shigella flexneri ATCC® 12022™ in .csv format)
3. Lipid profile MspExport.zip (Folder contains the batch files of the Escherichia coli ATCC® 11775™ and Shigella flexneri ATCC® 12022™ lipid profile reference spectra for the Bruker Biotyper database)
4. Lipid profile Bruker MALDI Biotyper Classification Results.pdf (File contains information about the classification of Escherichia coli ATCC® 11775™ and Shigella flexneri ATCC® 12022™ based on lipid profiles generated in the Bruker Biotyper database)
5. Protein profile MALDI MS Bruker files.zip (Folder contains MALDI MS spectral files of protein extracts from Escherichia coli ATCC® 11775™ and Shigella flexneri ATCC® 12022™ generated by Bruker microflex LT MALDI mass spectrometer readable in Bruker FlexAnalysis software)
6. Protein profile Bruker MALDI Biotyper Classification Results.pdf (File contains information about the classification of Escherichia coli ATCC® 11775™ and Shigella flexneri ATCC® 12022™ based on protein profiles generated in the Bruker Biotyper database)
METHODOLOGICAL INFORMATION
Description of methods used for collection/generation of data: Lipid extracts from Escherichia coli ATCC® 11775™ and Shigella flexneri ATCC® 12022™ bacteria were prepared according to protocol described by Bligh & Dyer (https://doi.org/10.1139/o59-099). Protein extracts from Escherichia coli ATCC® 11775™ and Shigella flexneri ATCC® 12022™ bacteria were prepared according to on-target extraction method (https://doi.org/10.1002/jms.4696).
Methods for processing the data: MALDI MS spectra of lipid extracts were obtained using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer Bruker ultrafleXtreme in positive-ion mode with reflector in range m/z 200-2000. MALDI MS spectra of protein extracts were obtained using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer Bruker microflex LT. The classifications was carried out using the Bruker Biotyper MBT Compass Library Revision H (Bruker Daltonik, Bremen, Germany).
Instrument- or software-specific information needed to interpret the data: Files in the "Lipid profile MALDI MS Bruker files.zip" and "Protein profile MALDI MS Bruker files.zip" folders can be opened with Bruker flexAnalysis 3.3 or later.
Standards and calibration information: Mass calibration was performed using external standard (cesium iodide, CsI) with a quadratic calibration strategy.
