0. SECTIONS
-------------
1. Project
2. Dataset
3. Terms of Use
4. Contents
5. Method and Processing

1. PROJECT
------------
Title: Invesitgating liquid AP-MALDI MS for the large-scale analysis of liquid samples.
Dates: September 2014/March 2018
Funding organisation: EPSRC, Waters Corporation
Grant no.: DTG no.1498422 

2. DATASET
------------
Title: Dataset to support liquid AP-MALDI MS profiling for mastitis detection.
Description:  The dataset supports the article by Hale, O. J. et al. (2019), 'Liquid atmospheric pressure Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry adds enhanced functionalities to MALDI MS profiling for disease diagnostics', in ACS Omega 4(7), 12759-12765, https://doi.org/10.1021/acsomega.9b01476. The dataset contains mass spectrometry data, multivariate models and validation reports.

Publication Year: 2018

Creator(s): Oliver J. Hale1, and Rainer Cramer1
Contributors: Michael Morris2, Barney Jones3, Chris Reynolds3
Organisation(s): 1:University of Reading 2: Waters Corporation 3: The Centre for Dairy Research, University of Reading.

3. TERMS OF USE
-----------------

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_projects_and_reports.zip
CID_MS_MS.zip
Healthy_samples.zip
Masitis_samples.zip

Files appended with the suffix *_dt.raw have been produced in the drift time domain. This helps to select the correct CID MS/MS fragment ions from the high complexity samples, since multiple ions may be selected even with a narrow quadrupole window.

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. Validation reports are provided as .pdf files.

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. 4.1; 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.
UniDec, freely available software from the University of Oxford website, is recommended for viewing, processing and deconvoluting protein mass spectra due to its advanced binning, smoothing and background subtraction methods.