SE129:/S3/M2

Sample Set Information

ID	TSE9
Title	MS-DIAL demo files
Description	Both data independent MS/MS acquisition (SWATH) and data dependent MS/MS acquisition (IDA) data sets is downloaded as the demo files of MS-DIAL. In order to use MS-DIAL program, the user has to convert the vendor's raw data to ABF file format. The demonstration for file convert can be performed via AB Sciex raw data sets (.wiff and .wiff.scan). The file converter is available at http://www.reifycs.com/english/AbfConverter/. If you want to demonstrate MS-DIAL itself, please use the converted files (.abf) from the below link. Also see http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/MSDIAL%20quick%20start.pdf
Authors	Hiroshi Tsugawa, Tomas Cajka, Tobias Kind, Yan Ma, Brendan Higgins, Kazutaka Ikeda, Mitsuhiro Kanazawa, Jean VanderGheynst, Oliver Fiehn & Masanori Arita
Reference	Tsugawa et al. (2015) Nature Methods 12(6):523–526
Comment

PubMed

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

Sample Information

ID	S3
Title	Chlorella sorokiniana (UTEX 2805)
Organism - Scientific Name	Chlorella sorokiniana
Organism - ID	NCBI taxonomy 3076
Compound - ID
Compound - Source
Preparation	UTEX 2341 (originally classified as Chlorella minutissima), Chlorella sorokiniana (UTEX 2805), and Chlorella variabilis (ATCC NC64A) were plated on ATCC #5 agar and colonies were selected for inoculation into liquid cultures. All three Chlorella strains were cultivated simultaneously in 250 mL hybridization tubes with four independent cultures per strain. Hybridization tubes were filled with 200 mL media and maintained in a 28 °C water bath. Aeration was supplied at 125 mL per minute with 2% CO2 mixed with air (v/v). Reactors were illuminated horizontally (10,000 lx) by T5 growth lamps operating on a 16:8 light/dark cycle and cultures were mixed by stir bar operating at ∼150 rpm. UTEX 2341 was cultivated in N8-NH4 medium30, C. sorokiniana in N8 medium31 and C. variabilis in N8-NH4 medium supplemented with 20 mg/L yeast extract. Culture samples (1 mL) were quenched for lipidomics analysis during the late log growth 00stage.
Sample Preparation Details ID
Comment	Tsugawa et al. (2015) Nature Methods 12(6):523–526

PubMed

Analytical Method Information

ID	M2
Title	IDA, Negative ion mode
Method Details ID	MS1
Sample Amount	5 µL
Comment

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

Analytical Method Details Information

ID	MS1
Title	LC-QTOF-MS/MS Method
Instrument	LC:Agilent 1290 MS:AB Sciex TripleTOF 5600+ system
Instrument Type	UPLC-QTOF-MS
Ionization	APCI
Ion Mode	Positive and Negative
Description	The liquid chromatography system consisted of an Agilent 1290 system (Agilent Technologies Inc.) with a pump (G4220A), a column oven (G1316C), and an autosampler (G4226A). For hydrophilic metabolite analysis, mobile phase A was 10 mM ammonium formate with 0.125 % formic acid in water; mobile phase B was 95:5 acetonitrile:water (v/v) with 10 mM ammonium formate and 0.125 % formic acid. An Acquity UPLC BEH Amide column (150×2.1 mm; 1.7 µm) coupled to a VanGuard BEH Amide pre-column (5×2.1 mm; 1.7 µm) (Waters; Milford, MA, USA) was used. The gradient was 0 min, 100% B; 2 min, 100% B; 7.7 min, 70% B; 9.5 min, 40% B; 10.3 min, 30% B; 12.8 min, 100% B; 16.8 min, 100% B. The column flow rate was 0.4 mL/min, autosampler temperature was 4 °C, injection volume was 2 µL, and column temperature was 45 °C. For lipid analysis, mobile phase A was 60:40 acetonitrile:water (v/v) with 10 mM ammonium formate and 0.1% formic acid; mobile phase B was 90:10 isopropanol:acetonitrile (v/v) with 10 mM ammonium formate and 0.1% formic acid. The lipidomic LC method utilized an Acquity UPLC charged-surface hybrid (CSH) C18 column (100×2.1 mm; 1.7 µm) coupled to an Acquity CSH C18 VanGuard pre-column (5×2.1 mm; 1.7 µm) (Waters; Milford, MA, USA). The gradient was 0 min, 15% B; 2 min, 30% B; 2.5 min, 48% B; 11 min, 82% B, 11.5 min, 99% B; 12 min, 99% B; 12.1 min, 15% B; 15 min, 15% B. The column flow rate was 0.6 mL/min, autosampler temperature was 4 °C, injection volume was 3 µL in positive mode and 5 µL in negative mode, and column temperature was 65 °C. Mass spectrometry was performed on an AB Sciex TripleTOF 5600+ system (Q-TOF) equipped with a DuoSpray ion source. All analyses were performed at the high sensitivity mode for both TOF MS and product ion scan. The mass calibration was automatically performed every 10 injections using an APCI positive/negative calibration solution via a calibration delivery system (CDS). For hydrophilic interaction chromatography analysis, SWATH (sequential window acquisition of all theoretical mass spectra) acquisition with positive ion mode was used as the data independent acquisition system. The SWATH parameters were MS1 accumulation time, 50 ms; MS2 accumulation time, 30 ms; collision energy, 45 V; collision energy spread, 15 V; cycle time, 640 ms; Q1 window, 25 Da; mass range, m/z 50–500. The other parameters were curtain gas, 35; ion source gas 1, 50; ion source gas 2, 50; temperature, 300 °C; ion spray voltage floating, 4.5 kV; declustering potential, 100 V; RF transmission, m/z 40: 33%, m/z 120: 33%, and m/z 390: 34%. For lipid analysis, six different methods were used; DDA (data-dependent acquisition) with positive ion mode, DDA with negative ion mode, SWATH acquisition (Q1 window, 21 Da) with positive ion mode, SWATH acquisition (Q1 window, 21 Da) with negative ion mode, SWATH acquisition (Q1 window, 65 Da) with positive ion mode, and SWATH acquisition (Q1 window, 65 Da). The common parameters in both SWATH/DDA and positive/negative ion mode were collision energy, 45 V; collision energy spread, 15 V; mass range, m/z 100–1250; curtain gas, 35; ion source gas 1, 60; ion source gas 2, 60; temperature, 350 °C; declustering potential, 80 V; RF transmission, m/z 80: 50%, m/z 200: 50%. The ion spray voltage floating of positive/negative ion mode were +5.5/–4.5 kV, respectively. The DDA parameters in both positive and negative ion modes were MS1 accumulation time, 100 ms; MS2 accumulation time, 50 ms; cycle time, 650 ms; dependent product ion scan number, 10; intensity threshold, 500; exclusion time of precursor ion, 5 s; mass tolerance, 20 mDa; ignore peaks, within 6 Da; dynamic background subtraction, TRUE. The SWATH parameters of 21/65 Da Q1 window were MS1 accumulation time, 100/50 ms; MS2 accumulation time, 10/30 ms; cycle time, 731/640 ms; Q1 window, 21/65 Da.
Comment_of_details	Tsugawa et al. (2015) Nature Methods 12(6):523–526

PubMed