Summary of Study ST000561

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000412. The data can be accessed directly via it's Project DOI: 10.21228/M8SS33 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST000561
Study Title	Exploring the link between genotype, phenotype and metabolome for tomato seed quality attributes
Study Type	Tomato Seed Metabolites Profiling (dry seed and 6 hour imbibed seeds comparision)
Study Summary	In this study the F8 population of 100 Recombinant Inbred Lines (RILs) obtained from a cross between Solanum lycopersicum X Solanum pimpinellifolium were intelligently allocated to two sub-populations optimized for the distribution of parental alleles using the R-procedure DesignGG (Li et al., 2009; Joosen et al., 2013); hence 50 RIL lines were used for dry seeds and 50 lines for 6h imbibed seeds
Institute	Wageningen University & Research
Department	Plant Physiology
Laboratory	Wageningen Seed Lab, Lab
Last Name	Ligterink
First Name	Wilco
Address	Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
Email	wilco.ligterink@wur.nl
Phone	31 317 48 28 09
Submit Date	2017-02-07
Num Groups	1
Total Subjects	100
Publications	Metabolomic analysis of tomato seed germination, Metabolomics DOI: 10.1007/s11306-017-1284-x
Analysis Type Detail	GC-MS
Release Date	2017-10-25
Release Version	1

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Sample Preparation:

Sampleprep ID:	SP000590
Sampleprep Summary:	The extraction method is modified from the method previously described by (Roessner et al., 2000). Approximately a bulk of approximately 70-100 seeds (30mg) seeds were homogenized in 2 ml tubes with 2 iron balls (2.5mm), pre-cooled in liquid nitrogen. For the homogenization the micro-dismembrator (Sartorius) is used at 1500 rpm. 700μl methanol/ chloroform (4:3) was added together with the standard (0.2mg/ml ribitol) and mixed thoroughly. After 10 minutes sonication, 200μl MQ was added to the mixture followed by vortexing and centrifuging (5 mins 13,500rpm). Methanol phase was collected in a glass vial. 500μl methanol/chloroform was added to the remaining organic phase and kept on ice for 10 minutes. 200μl MQ was added followed by vortexing and centrifuging (5 mins 13,500rpm). Again, the methanol phase was collected and mixed with the other collected phase. 100μl was dried overnight in a speedvac (35°C Savant SPD121). The GC-TOF-MS method was previously described by (Carreno-Quintero et al., 2012) with some minor modifications. Detector voltage was set at 1600V. Raw data was processed using the chromaTOF software 2.0 (leco instruments) and further processed using the Metalign software (Lommen, 2009), to extract and align the mass signals. A signal-to-noise ratio of 2 was used. The output was further processed by the Metalign Output Transformer (METOT; Plant Research International, Wageningen) and the mass signals that were present in less than 3 RILs were discarded. Out of all the mass signals, centrotypes are formed using the MSclust program (Tikunov et al., 2011). This resulted in 160 unique centrotypes (representative masses). The mass spectra of these centrotypes were used for identification by matching to an in-house constructed library, the NIST05 (National Institute of Standards and Technology, Gaithersburg, MD, USA; http://www.nist.gov/srd/mslist.htm) and Golm libraries (http://csbdb.mpimp-golm.mpg.de/csbdb/gmd/gmd.html)). This identification is based on spectra similarity and comparison with retention indices calculated by using a 3rd order polynomial function (Strehmel et al., 2008).
Sampleprep Protocol Filename:	SL_COL_PROT.pdf
Processing Method:	For the homogenization the micro-dismembrator (Sartorius) is used at 1500 rpm
Cell Type:	Seeds