SE133:/S1/M1/D1

Sample Set Information

ID	TSE7
Title	Regular expressions of MS/MS spectra for partial annotation of metabolite features
Description	Partial annotation and characterization of metabolite structures on the basis of data from tandem mass spectrometry (MS/MS) spectra are technical bottlenecks in metabolomics. Novel approaches should be explored for evaluation of spectral similarities among structurally related compounds as well as for description of fragmentation motifs commonly observed in MS/MS spectra.
Authors	Fumio Matsuda
Reference	Matsuda (2016) Metabolomics, July, 12:113
Comment	MS/MS strings of MassBank dataset and MS/MS strings of Arabidopsis (ATH) and rice (OSA) MS/MS spectra data are stored in DROP Met as "Test dataset for the regular expression of MS/MS spectra data"

doi: 10.1007/s11306-016-1052-3

The raw data files are available at DROP Met web site in PRIMe database of RIKEN.

Sample Information

ID	S1
Title	Arabidopsis thaliana
Organism - Scientific Name	Arabidopsis thaliana
Organism - ID	NCBI taxonomy 3702
Compound - ID
Compound - Source
Preparation	Seedlings of Arabidopsis thaliana (Col-0) were grown in pots containing soil at 20°C with a 16 h daily photoperiod. Six weeks after germination, the 12th or 13th expanded rosette leaves (rosette leaf), the 1st and 2nd expanded cauline leaves (cauline leaf), the upper part of the inflorescence (inflorescence), and first internode tissues (stem) were collected from eight individual Arabidopsis plants at stage 6.3 (Boyes et al., 2001) and stored at −80°C until use. For metabolic phenotyping of Ds transposon insertion lines (Kuromori et al., 2004, 2006), 60lines of homozygous seeds were grown on the half‐strength MS medium plates at 20°C with a 16h daily photoperiod. Two weeks after germination, whole tissues of 20 seedlings were collected, weighed, and stored at −80°C.
Sample Preparation Details ID
Comment	Matsuda et al (2009) Plant J 57: 555–577.

PubMed

Analytical Method Information

ID	M1
Title	LC-QTOF-MS
Method Details ID	MS1
Sample Amount	3 μL
Comment

Analytical Method Details Information

ID	MS1
Title	LC-QTOF-MS Method
Instrument	Waters Acquity UPLC system; MS, Waters Q-Tof Premier
Instrument Type	UPLC-QTOF-MS
Ionization	ESI
Ion Mode	Positive
Description	The frozen tissues were homogenized in five volumes of 80% aqueous methanol containing 0.1% acetic acid, 0.5 mg/L of lidocaine, and d-camphor sulfonic acid (Tokyo Kasei) using a mixer mill (MM 300, Retsch) with a zirconia bead for 6 min at 20 Hz. Following centrifugation at 15,000g for 10 min and filtration (Ultrafree-MC filter, 0.2 μm, Millipore), the sample extracts were applied to an HLB μElution plate (Waters) equilibrated with 80% aqueous methanol containing 0.1% acetic acid. The eluates (3 μL) were subjected to metabolome analysis using LC-ESI-Q-TOF/MS. Metabolome analysis was performed with an LC-ESI-Q-TOF/MS system equipped with an ESI interface (HPLC: Waters Acquity UPLC system; MS: Waters Q-TOF Premier) operated under previously described conditions (Matsuda et al., 2009). In the negative ion mode, the MS conditions were as follows: capillary voltage: +3.0 keV; cone voltage: 22.5 V; source temperature: 120°C; desolvation temperature: 450°C; cone gas flow: 50 L/h; desolvation gas flow: 800 L/h; collision energy: 2 V; detection mode: scan (m/z 100–2,000; dwell time: 0.45 s; interscan delay: 0.05 s, centroid); dynamic range enhancement mode: on. The scans were repeated for 19.5 min in a single run.
Comment_of_details	Matsuda et al. Plant Physiol.(2010) Feb;152(2):566-78

PubMed

Data Analysis Information

ID	D1
Title	Data analysis
Data Analysis Details ID	DS1
Recommended decimal places of m/z
Comment

Data Analysis Details Information

ID	DS1
Title	Methods
Description	2.1 MS/MS spectra MassBank data with fragment assignment information (Fragment ion and neutral loss matrix) were obtained from Metabolime.jp (http://metabolomics.jp/wiki/Index:MassBank) (Arita and Suwa 2008; Horai et al. 2010). All procedures were based on in-house scripts written in Perl 5.12. Similarity networks were visualized by Cytoscape 3.2.1 (Shannon et al. 2003). All MS/MS spectral libraries obtained from various tissues of Arabidopsis (ATH06p–ATH014p) (Matsuda et al. 2010) and rice cultivars (OSA06p–OSA014p) (Matsuda et al. 2012) were downloaded from the PRIME webpage (http://prime.psc.riken.jp/, Supplementary Table S1) (Sakurai et al. 2013). Each entry in the MS/MS spectral library has a unique ID such as ATH14p11717 (Matsuda et al. 2009). For visualization and analysis of these MS/MS spectra, (1) please go to the MS2T section of the RIKEN PRIMe web page (http://prime.psc.riken.jp/lcms/ms2tview/ms2tview.html), (2) input IDs (e.g., ATH14p11717) into the “MS/MS spectrum tag(MS2T) accession codes” field, and (3) press the Start button. (4) A list of MS/MS spectra will appear. (5) Press the Detail:[ATH14p11717] button for detailed analysis of the MS/MS spectra. The “Molecular formula search” function is also available. 2.2 Conversion of MS/MS spectra to MS/MS strings MS/MS strings were generated from the MS/MS spectra by the following procedure. For each entry in the MS/MS spectral libraries, 1. The entry was discarded when intensity of the most intense fragment (base peak) was less than 30 counts per second. 2. The fragments whose intensity was less than that of the 12th most intense signal were ignored. Fragment signals of weak intensity (less than 1.0 % of the base peak) were also ignored. 3. The chemical formula of precursors was assigned according to the seven golden rules (Kind and Fiehn 2007). 3.1 The chemical formulas including CHONS atoms with 0 ≤ N ≤ 5 and 0 ≤ S ≤ 3 were considered. All formulas within the threshold (10 mDa [m/z < 500] and 20 ppm [m/z > 500]) were used to construct MS/MS strings. 3.2 For each chemical formula of a precursor, the chemical formulas of all fragments were deduced according to the seven golden rules, with the threshold at 20 ppm. The numbers of atoms in a molecular fragment had to be less than those in the precursor. 3.3 The total intensity of fragment signals whose chemical formulas were successfully elucidated (I selected) was calculated. The chemical formula of a precursor was accepted when I selected ÷ I total was greater than 0.8, where I total indicates total intensity of all fragment signals (Meringer and Schymanski 2013). 4. An entry without an accepted chemical formula of a precursor was discarded. 5. All possible MS/MS strings were generated using the following format: [formula of neutral loss 1]:[formula of fragment 1];[formula of neutral loss 2]:[formula of fragment 2];… [formula of neutral loss n]:[formula of fragment n];. 5.1 The threshold for finding a chemical formula of a neutral loss was 15 mDa. 5.2 One neutral loss involving negative atom numbers (such as; C1H-2:) was allowed in 1 MS/MS string. 5.3 One fragment with an integer index of hydrogen deficiency (IHD) was allowed in 1 MS/MS string. The MS/MS strings that were generated by this procedure were incomplete because steps 5.2 and 5.3 are heuristic conditions designed to restrict a combinatorial explosion of the number of MS/MS strings. All MS/MS string libraries derived from MassBank, Arabidopsis, and rice data were downloaded from the project homepage (http://www-shimizu.ist.osaka-u.ac.jp/hp/en/software/regex.html) and DROP Met in PRIMe website (http://prime.psc.riken.jp/?action=drop_index).
Comment_of_details	MS/MS strings of MassBank dataset (Supplementary Data 1) and MS/MS strings of Arabidopsis (ATH) and rice (OSA) MS/MS spectra data. http://prime.psc.riken.jp/archives/data/DropMet/022/

The raw data files are available at DROP Met web site in PRIMe database of RIKEN.

The peak data files of this analysis are available at MS2T.