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

1. PROJECT
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Title: Development of a Novel MALDI Mass Spectrometer and Technology for the Generation of Multiply Charged Ions at High Sensitivity
Dates: 01 February 2014/31 January 2017
Funding organisation: EPSRC
Grant no.: EP/L006227/1

2. DATASET
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Title: Dataset supporting a project of developing a nanoHPLC-MALDI MS/MS workflow employing CID of multiply charged proteolytic peptides for bottom-up proteomics
Description:  Dataset contains two sets of LC-MALDI MS/MS runs performed on an in-house developed AP-MALDI source attached to a commercial mass spectrometer, as well as a complementary LC-ESI MS/MS dataset. Other data include experiments on AP-MALDI MS signal duration and MS/MS experiments.

Publication Year: 2016

Creator(s): Pavel Ryumin, Rainer Cramer
Organisation(s): University of Reading

3. TERMS OF USE
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This dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/.

4. CONTENTS
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File listing
ESI.zip
FA.zip
TFA.zip
signal_duration.zip

All data is obtained using proprietary software MassLynx (Waters) and stored using close source proprietary data format. 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. 

5. METHOD and PROCESSING
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The dataset contains data that was generated using a commercial mass spectrometer Synapt-G2Si (Waters) equipped with an in-house developed AP-MALDI ion source. 
Masslynx software (ver. 4.1; Waters) was used to collect and process the data.
Only the data starting with [ESI, FA, TFA] was processed to compensate systematic mass accuracy errors. For this the “Modify Calibration” method within MassLynx software was used. All data files contain a _HEADER file with relevant instrument settings and employed methods recorded.
Manuscript in preparation at time of data deposit entitled "A nanoHPLC-MALDI MS/MS workflow employing CID of multiply charged proteolytic peptides for bottom-up proteomics" by P.Ryumin, J.Brown, M.Morris, R.Cramer contains the methods section where the exact procedures of data acquisition are described.