This HAWKSWORTHreadme.txt file was generated on 2018-11-22 by Ed Hutchinson ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Proteomics as a tool for Live Attenuated Influenza Vaccine characterisation 2. Author Information Amy Hawksworth (1), Mahesh Jayachander (1); Svenja Hester (2), Shabaz Mohammed (2) and Edward Hutchinson (3)*. (1) Flu-BPD, MedImmune, Plot 7 Renaissance Way, Speke, Liverpool L24 9JW, United Kingdom. (2) Advanced Proteomics Facility, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom. (3) MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom. *Principal Investigator Contact Information Name: Edward Hutchinson Institution: MRC-University of Glasgow Centre for Virus Research Address: Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom Email: edward.hutchinson@glasgow.ac.uk 3. Date of data collection (single date, range, approximate date) 2015-09-06 to 2015-12-14 4. Geographic location of data collection (where was data collected?): Samples were collected at Flu-BPD, MedImmune (Plot 7 Renaissance Way, Speke, Liverpool L24 9JW, United Kingdom) and mass spectrometry performed at the Advanced Proteomics Facility, Department of Biochemistry, University of Oxford (South Parks Road, Oxford OX1 3QU, United Kingdom). 5. Information about funding sources that supported the collection of the data: Edward Hutchinson was funded by an MRC Career Development Award [MR/N008618/1] and by an MRC programme [Grant MR/K000241/1] awarded to Ervin Fodor (University of Oxford). -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC BY 4.0 2. Links to publications that cite or use the data: Pending (pre-submission data deposition) 3. Links to other publicly accessible locations of the data: N/A 4. Links/relationships to ancillary data sets: N/A 5. Was data derived from another source? N/A 6. Recommended citation for the data: Pending (pre-submission data deposition) --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: Hawksworth et al Processed Data.xlsx Short description: Excel workbook containing a detailed overview of all other related files and experimental design (‘Overview’ sheet), a list of viral titres for samples (‘Titres’ sheet) and, as described in the overview, five sheets containing processed data for samples analysed for each of five different viruses. B. Filenames within the folder ‘Mass Spectra Raw Files’: Qex03_SVH_151214_MedImmune_Bol_PHF1.raw, Qex03_SVH_151214_MedImmune_Bol_CHF1.raw, Qex03_SVH_151214_MedImmune_Bol_DCP1.raw, Qex03_SVH_151214_MedImmune_Bol_MVB1.raw (within the sub-folder A_Bol); Qex03_SVH_151207_MedImmune_CALIF_PHF1.raw, Qex03_SVH_151207_MedImmune_CALIF_PHF2.raw, Qex03_SVH_151207_MedImmune_CALIF_PHF3.raw, Qex03_SVH_151207_MedImmune_CALIF_CHF1.raw, Qex03_SVH_151207_MedImmune_CALIF_DCP1.raw, Qex03_SVH_151207_MedImmune_CALIF_MVB1.raw, Qex03_SVH_151207_MedImmune_CALIF_NAF2.raw, Qex03_SVH_151207_MedImmune_CALIF_NAF3.raw (within the sub-folder A_Cal); Qex03_SVH_150906_MedImmune_PHF.raw, Qex03_SVH_150921_MedImmune_PHF.raw, Qex03_SVH_150921_MedImmune_PHFb.raw, Qex03_SVH_151207_MedImmune_TX_PHF2.raw, Qex03_SVH_151207_MedImmune_TX_PHF3.raw, Qex03_SVH_150906_MedImmune_CHF.raw, Qex03_SVH_150921_MedImmune_CHF.raw, Qex03_SVH_150906_MedImmune_DCP.raw, Qex03_SVH_150921_MedImmune_DCP.raw, Qex03_SVH_150906_MedImmune_MVB.raw, Qex03_SVH_150921_MedImmune_MVB.raw, Qex03_SVH_151207_MedImmune_TX_NAF2.raw, Qex03_SVH_151207_MedImmune_TX_NAF3.raw (within the sub-folder A_Tex); Qex03_SVH_151214_MedImmune_Bris_PHF2.raw, Qex03_SVH_151214_MedImmune_Bris_PHF3.raw, Qex03_SVH_151214_MedImmune_Bris_NAF2_151215145159.raw, Qex03_SVH_151214_MedImmune_Bris_NAF3 (within the sub-folder B_Bris); Qex03_SVH_151207_MedImmune_Mass_PHF1.raw, Qex03_SVH_151207_MedImmune_Mass_PHF2.raw, Qex03_SVH_151207_MedImmune_Mass_PHF3.raw, Qex03_SVH_151207_MedImmune_Mass_CHF1.raw, Qex03_SVH_151207_MedImmune_Mass_DCP1.raw, Qex03_SVH_151207_MedImmune_Mass_MVB1.raw, Qex03_SVH_151207_MedImmune_Mass_NAF2.raw and Qex03_SVH_151207_MedImmune_Mass_NAF3.raw (within the sub-folder B_Mass). Short description: Mass spectrometry raw files C. Filenames within the folder ‘Proteome databases’: A_Bolivia_559_2013.fasta, A_California_07_2009.fasta, A_Texas_50_2012.fasta, B_Brisbane_60_08.fasta, B_Massachussetts_2_2012.fasta, Gallus gallus UP000000539 2017-05-16 noUb.fasta, Standards MS QualQuant Mix.fasta and Ubiquitin.fasta Short description: Proteome lists Short description: Mass spectrometry raw files D. Filenames within the folder ‘Outputs from analysis’: in each of five subfolders (A_Bol, A_Cal, A_Tex, B_Bris and B_Mass) the files mqpar.xml, proteinGroups.txt and summary.txt Short description: Outputs from Maxquant data analysis, as described in (A) Overview. 2. Relationship between files: Described in (A) Overview. Briefly, the raw data in (B) were compared to the proteome lists in (C) to produce the data in (D), which was futher analysed and interpreted in the spreadsheet (A). 3. Additional related data collected that was not included in the current data package: None included. 4. Are there multiple versions of the dataset? no -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Refer to the Overview sheet of ‘Hawksworth et al Processed Data.xlsx’ and to the accompanying paper Hawksworth et al. ‘Proteomics as a tool for Live Attenuated Influenza Vaccine characterisation.’ 2. Methods for processing the data: Refer to the Overview sheet of ‘Hawksworth et al Processed Data.xlsx’ 3. Instrument- or software-specific information needed to interpret the data: Refer to the Overview sheet of ‘Hawksworth et al Processed Data.xlsx’ and to the accompanying paper Hawksworth et al. ‘Proteomics as a tool for Live Attenuated Influenza Vaccine characterisation.’