The following flat-files describe the metadata input for the exemplar merging pipeline. They are required in order to identify the variable and observations within the input files so that appropriate statistical analysis can be applied. They are also important for the metadata required in the MzQuantML XML export.
[Dataset] name: Comparison of sodium dodecyl sulfate vs octyl glucoside [Organisation] name: SynthSys address: SynthSys, University of Edinburgh, Waddington Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JD, UK url: http://www.synthsys.ed.ac.uk [Organisation] name: ISMB address: Institute of Structural and Molecular Biology, University of Edinburgh, Edinburgh, UK url: http://www.ed.ac.uk/schools-departments/biology/structural-molecular-biology [Author] id: JK fistname: Johanna surname: Krahmer email: J.Krahmer@sms.ed.ac.uk affiliation: SynthSys affiliation: ISMB [Experiment] #.* means everything is part of the same experiment (it matches everything) pattern: .* name: SDS vs OG description: A comparison of sodium dodecyl sulfate vs octyl glucoside author: JK [Variable] #regular expression matches the letters before the final replicate tag see http://www.regexplanet.com/advanced/java/index.html pattern: _([a-zA-Z0-9]+)_\d$ id: treatment name: treatment description: treatment class: java.lang.String [Replicates] # $ is the end of the header and () is the area to match...so this pattern matches everything that is after the _ and before the end of the header pattern: _(\d+)$ [Headers] 3702_EthylAcetate_OGeth_1 3702_EthylAcetate_OGeth_2 3702_EthylAcetate_OGeth_3 3702_EthylAcetate_OGeth_4 3702_EthylAcetate_OGeth_5 3702_EthylAcetate_SDSeth_1 3702_EthylAcetate_SDSeth_2 3702_EthylAcetate_SDSeth_3 3702_EthylAcetate_SDSeth_4 3702_EthylAcetate_SDSeth_5
[Dataset] name: IC261 [Organisation] name: SynthSys address: SynthSys, University of Edinburgh, Waddington Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JD, UK url: http://www.synthsys.ed.ac.uk [Organisation] name: ISMB address: Institute of Structural and Molecular Biology, University of Edinburgh, Edinburgh, UK url: http://www.ed.ac.uk/schools-departments/biology/structural-molecular-biology [Author] id: TLB fistname: Thierry surname: Le Bihan email: thierry.lebihan@ed.ac.uk affiliation: SynthSys affiliation: ISMB [Author] id: SFM fistname: Sarah initials: F surname: Martin email: Sarah.Martin@ed.ac.uk affiliation: SynthSys [Author] id: GVO fistname: Gerben initials: surname: van Ooijen email: Gerben.vanOoijen@ed.ac.uk affiliation: SynthSys [Experiment] #.* means everything is part of the same experiment (it matches everything) pattern: .* name: IC261 description: IC261 author: GVO, SFM, TLB [Variable] #matches the letters before the final replicate tag see http://www.regexplanet.com/advanced/java/index.html pattern: _([a-zA-Z0-9]+)_\d$ id: treatment name: treatment description: treatment class: java.lang.String [Replicates] # $ is the end of the header and () is the area to match...so this pattern matches everything that is after the _ and before the end of the header pattern: _(\d+)$ [Headers] 120905_o1_04_ph120831_ot_CCAI_3 120905_o1_05_ph120831_ot_CCAI_2 120905_o1_08_ph120831_ot_CCAI_4 120906_o1_02_ph120831_ot_CCAI_5 120906_o1_06_ph120831_ot_CCAI_1 120905_o1_03_ph120831_ot_IC261_5 120905_o1_07_ph120831_ot_IC261_2 120906_o1_03_ph120831_ot_IC261_3 120906_o1_07_ph120831_ot_IC261_4 120906_o1_09_ph120831_ot_IC261_1
The following metadata describes the experiment by Docherty (2010) and is required for the import of MaxQuant and Progenesis files into the merging workflow.
[Dataset] name: MusPhospho [Organisation] name: SynthSys address: SynthSys, University of Edinburgh, Waddington Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JD, UK url: http://www.synthsys.ed.ac.uk [Organisation] name: ISMB address: Institute of Structural and Molecular Biology, University of Edinburgh, Edinburgh, UK url: http://www.ed.ac.uk/schools-departments/biology/structural-molecular-biology [Author] id: TLB firstname: Thierry surname: Le Bihan email: thierry.lebihan@ed.ac.uk affiliation: SynthSys affiliation: ISMB [Experiment] #the regular expression “.*” means everything is part of the same experiment (it matches everything) pattern: .* name: MusPhospho description: MusPhospho author: TLB [Variable] # the regular expression matches the letters before the final replicate tag see http://www.regexplanet.com/advanced/java/index.html pattern: _([a-z])\d$ id: slice name: slice description: slice class: java.lang.String [Replicates] # $ is the end of the header and “()” is the area to match. This pattern matches everything that is after the _ and before the end of the header pattern: _[a-z](\d+)$ [Headers] 090319_o1_02_so090213ph_mo_c1 090319_o1_03_so090213ph_mo_c2 090319_o1_04_so090213ph_mo_s1 090319_o1_05_so090213ph_mo_s2