readme.txt 30/5/16 Fumio Matsuda Osaka University, RIKEN CSRS This folder consists of two datasets. 1. MS/MS strings of MassBank dataset. 2. MS/MS strings of Arabidopsis and rice MS/MS spectra data. ************* 1. MS/MS strings of MassBank dataset. File:MassBank_MSMSsting_SupplementaryData1.txt The MS/MS spectrum of the proton adduct molecule ([M+H]+) of L-histidine (MassBank record, PR100321) could be described as the following MS/MS string by ignoring the signal intensity information: MS/MS spectrum: MS$FOCUSED_ION: PRECURSOR_M/Z 156.07727 MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+ PK$PEAK: m/z int. rel.int. 83.0607 153.7 171 93.0449 107.1 119 110.0715 896.6 999 156.0773 227.5 253 MS/MS string: C4H7N2:C4H7N2;C1H-2:C5H5N2;NH3:C5H8N3;C1H2O2:C6H10N3O2; The MS/MS string consists of a sequence of expressions like [chemical formula of neutral losses]:[chemical formula of fragment signals];. The MS/MS string is considered a full complete MS/MS string with 4 signals because it fully covers whole spectra (from m/z 0 to a precursor) and completely includes all 4 fragment signals within the region. Furthermore, several full incomplete (ignoring one or more fragments in full strings) or partial MS/MS strings could be generated from the MS/MS spectrum of L-histidine such as: Full incomplete C5H5N2:C5H5N2;NH3:C5H8N3;C1H2O2:C6H10N3O2; Partial NH3:C5H8N3;C1H2O2:C6H10N3O2; The MassBank records, whose fragment signals were manually assigned with a chemical formula, are available from Metabolomics.jp (http://metabolomics.jp/wiki/Index:MassBank) (Arita, Suwa 2008; Horai et al. 2010). This file includes a dataset including all full complete and full incomplete MS/MS strings longer than 2 signals was generated from the MassBank records with fragment assignments. Arita, M., K. Suwa (2008). Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database. BioData Min 1, 7 Horai, H., et al. (2010). MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom 45, 703-14 2. MS/MS strings of Arabidopsis and rice MS/MS spectra data. MS/MS spectra libraries including thousands of entries obtained from various tissues of Arabidopsis thaliana and rice cultivars, and other plant species using the data-dependent acquisition of tandem mass spectromete have been available in the public domain (http://prime.psc.riken.jp/lcms/ms2tview/list.html). Following MS/MS spectra libraries were converted into libraries of MS/MS strings. Files: ATHXXp.txt ATHXXp_MS/MSstring.txt OSAXXp.txt OSAXXp_MS/MSstring.txt (XX = 06.07,08,09,10,11,12,13 and 14) Library ID Spieces Accession Tissue Growth condition Number of records ATH06p Arabidopsis thaliana Col-0 Buds 4-week-old 10477 ATH07p Arabidopsis thaliana Col-0 Cauline leaves 4-week-old 9274 ATH08p Arabidopsis thaliana Col-0 Flowers 4-week-old 10879 ATH09p Arabidopsis thaliana Col-0 Rosette leaves (1st-5th) 4-week-old 9867 ATH10p Arabidopsis thaliana Col-0 Rosette leaves (5th-10th) 3-week-old 7506 ATH11p Arabidopsis thaliana Col-0 Silique 4-week-old 9938 ATH12p Arabidopsis thaliana Col-0 Internodes (1st and 2nd) 4-week-old 9305 ATH13p Arabidopsis thaliana Col-0 Seeds 4-week-old 12395 ATH14p Arabidopsis thaliana Col-0 Roots 4-week-old 10439 OSA06p Oryza sativa Habataki Leaf blade 2-week-old, Soil grown 7084 OSA07p Oryza sativa Sasanishiki/Habataki BILs mixture Leaf blade 2-week-old, Soil grown 6050 OSA08p Oryza sativa Sasanishiki/Habataki BILs mixture Leaf blade 2-week-old, Soil grown 5981 OSA09p Oryza sativa Sasanishiki/Habataki BILs mixture Leaf blade 2-week-old, Soil grown 6110 OSA10p Oryza sativa Sasanishiki/Habataki BILs mixture Leaf blade 2-week-old, Soil grown 6825 OSA11p Oryza sativa Sasanishiki/Habataki BILs mixture Leaf blade 2-week-old, Soil grown 7170 OSA12p Oryza sativa Sasanishiki/Habataki BILs mixture Leaf blade 2-week-old, Soil grown 7017 OSA13p Oryza sativa Sasanishiki/Habataki BILs mixture Leaf blade 2-week-old, Soil grown 6722 OSA14p Oryza sativa Sasanishiki/Habataki BILs mixture Leaf blade 2-week-old, Soil grown 7097 *************