CM name	LC technique	Column	pH	Eluents:	Eluent additives:	Description
AjsUoB	HILIC	Accucore 150 Amide HILIC	N/A	ACN(10mM Ammonium Formate, 0.1% Formic Acid): ACN/Water(95:5,v/v)(10mM Ammonium Formate, 0.1% Formic Acid)	10mM ammonium formate, 0.1% Formic Acid	NA
FEM_long	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18	Acidic	Water:MeOH	0.1% Formic Acid	An ACQUITY UPLC 1.8 lm 2.1 9 100 mm HSS T3 column (Waters) at 30C was eluted with a gradient program starting from 100% A (water, 0.1% formic acid) from 0 till 6 min and then increasing linearly over 56 min to 100% B (methanol, 0.1% formic acid) where it was held isocratic until 60 min, with a 0.3 ml/min ﬂow rate. Ref:10.1007/s11306-011-0298-z
FEM_lipids	Reversed-phase	Ascentis Express C18	Acidic	(60:40 water:ACN):(90:10 IPA:ACN)	10mM NH4COOH + 0.1% Formic Acid	Separation was performed using a HPLC Dionex (Thermo Fisher Scientific Germany), with a RP Ascentis Express (15 cm X 2.1 mm; 2.7 μm C18) purchased from Sigma (Milan, Italy). Column temperature was set at 55 °C using a Peltier effect column oven (Dionex Thermo Fisher Scientific Germany). Samples were injected using an autosampler (Dionex Thermo Fisher Scientific Germany) thermostated at 10°C. Separation was carried out following a 30 min multistep linear gradient as reported by Hu et al [24]. From 0-1.5 min isocratic elution with 32% B; from 1.5 to 4 min increase to 45% B, then to 52% B in 1 min, to 58% B in 3 min, to 66% B in 3 min, to 70% B in 3 min, to 75% B in 4 min, to 97% B in 3 min, then 97% B was maintained for 4 minutes. From 25.0 to 25.1 min solvent B was decreased to 32% and then maintained for another 4.9 min for column re-equilibration. Total duration of the analysis was 30 minutes, including the post-time. The flow-rate was 0.26 mLmin-1, the mobile phase A consisted of ACN 40%, NH4COOH 10 mM and HCOOH 0.1% and B consisted of IPA 90%, ACN 10%, NH4COOH 10 mM and HCOOH 0.1%. The HPLC system was coupled directly to an API 5500 triple-quadrupole mass spectrometer (Applied Biosystems/MDS Sciex, Toronto, Canada) equipped with a Electro Spray source. AnalystTM software version 1.6.1 (Applera Corporation, Norwalk, CT, USA) was used for instrument control and data acquisition
Life_old	Reversed-phase	Waters ACQUITY UPLC BEH C18	Acidic	Water:(20:80 acetone:ACN)	0.1% Formic Acid	A 1.7 μm 2.1 mm × 100 mm C18 BEH column (Waters) operated with a 6.0 min linear gradient from 0.1% formic acid in water to 0.1% formic acid in 20:80 acetone:acetonitrile. Ref: 10.1016/j.aca.2011.12.065
Life_new	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18	Acidic	Water:(30:70 MeOH:ACN)	0.1% Formic Acid	The mobile phase was 0.1 % formic acid in milli-Q® water (A) and 0.1 % formic acid in 30:70 (v/v) MeOH:ACN (B). A mobile phase concentration gradient from (A) to (B) was applied in a total run time of 7 min together with a flow gradient. Ref: 10.1016/j.aca.2011.12.065
RIKEN	Reversed-phase	Waters ACQUITY UPLC BEH C18	Acidic	Water:ACN	0.1% Formic Acid	The UPLC (Waters) conditions were manually optimized based on the separation patterns of 12 methionine-derived glucosinolates and were as follows: fl ow rate 0.24 ml min –1 ; solvents A, 0.1% formic acid in water and B, 0.1% formic acid in acetonitrile; gradient program of B (0 min, 0%; 0.25 min, 0%; 0.4 min, 9%; 0.8 min, 17%; 1.9 min, 100%; 2.1 min, 100%; 2.11 min, 0%); 3 min cycles with a temperature of 38°C. The TQMS detection conditions were the same as those for FIA-TQMS, except that the source temperature was 130°C. Ref: 10.1093/pcp/pcn183
Eawag_XBridgeC18	Reversed-phase	XBridge C18 3.5u 2.1x50 mm	Acidic	Water:MeOH	0.1% Formic Acid	The HPLC system consisted of a PAL Autosampler (CTC Analytics, Zwingen, Switzerland), a Rheos 2200 quaternary low pressure mixing pump (Flux Instruments, Basel, Switzerland), and an XBridge C18 column (3.5 μm, 2.1 × 50 mm) from Waters (Milford, U.S.) with a 2.1 × 10 mm precolumn of the same material. The gradient (water/methanol, both with 0.1% formic acid) was 90:10 at 0 min, to 50:50 at 4 min, to 5:95 at 17 min, held until 25 min then 90:10 at 25.1 to 30 min at a flow of 200 μL/min and a column temperature of 30 °C. Ref: 10.1021/es4044374; 10.1002/jms.3131
BfG_NTS_RP1	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um)	Acidic	Water:ACN	0.1% Formic Acid	Ref:10.1016/j.chroma.2015.11.014
HILIC_BDD_2	HILIC	Merck SeQuant ZIC-HILIC	N/A	ACN(0.1% formic acid):water(16 mM ammonium formate)	016 mM ammonium formate in water; 0.1% formic acid in ACN	Phase A: 100% eau + 16 mM Ammonium formiate Phase B: 100% ACN + 0,1% FA Flow: 0.25 ml/min Column temperature: 25°C Gradient: 0 to 2 min :97 % B 2 to 10 min :70 % B 10 to 15 min : 10 % B 15 to 17 min : 10 % B 17 to 18 min :97 % B 18 to 25 min : 97 % B
UniToyama_Atlantis	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um)	Acidic	ACN:Water	0.1% Formic Acid	Ref: www.massbank.eu
BDD_C18	Reversed-phase	Hypersil Gold 1.9 µm C18	Acidic	Water:ACN	0.1% Formic Acid	Phase A: 100% eau + 0,1% FA Phase B: 100% ACN + 0,1% FA Flow: 0.4 ml/min Column temperature: 40°C Gradient: 0 to 1 min : 0 % B 1 to 11 min :100 % B 11 to 13 min : 100 % B 13 to 14 min : 0 % B 14 to 16 min :0 % B
RPMMFDA	Reversed-phase	Waters ACQUITY UPLC BEH C18	Acidic	Water:ACN	0.1% Formic Acid	N/A
SNU_RIKEN_POS	Reversed-phase	Waters ACQUITY UPLC BEH C18	Acidic	Water:ACN	0.1% Formic Acid	N/A
UFZ_Phenomenex	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex	Acidic	Water:MeOH	0.1% Formic Acid	Ref: www.massbank.eu
MTBLS87	HILIC	Merck SeQuant ZIC-pHILIC column	Alkaline	ACN:Water	Ammonium carbonate	LC separation was performed on a ZIC-pHILIC column (Merck SeQuant; 150 × 2.1 mm, 5 µm particle size). Acetonitrile (A) and 10 mM ammonium carbonate buffer, pH 9.3 (B) were used as the mobile phase, with gradient elution from 80% A to 20% A in 30 min and 100 µl/min flow rate. Sample injection volume was 1 µl per run.
KI_GIAR_zic_HILIC_pH2_7	HILIC	Merck SeQuant ZIC-HILIC	2.7	ACN:Water	0.1% Formic Acid	Polar metabolites were separated on a HILIC SeQuant ZIC-HILIC (Merck, Darmstadt, Germany) column 100 Å (100 × 2.1 mm, 3.5 μm particle size) coupled to a guard column (2.1 × 2 mm, 3.5 μm particle size) and an inline-filter. Sample analysis in positive ionization mode was performed using water with 0.1% formic acid (solvent A) and acetonitrile with 0.1% formic acid (solvent B). The elution gradient used was as follows: isocratic step at 95% B for 1.5 min, 95 to 40% B in 12 min, maintained at 40% B for 2 min, then decreasing to 25% B at 14.2 min, maintained for 2.8 min, then returned to initial conditions over 1 min, and then the column was equilibrated at initial conditions for 7 min. The flow rate was 0.3 mL/min; injection volume was 2 μL, and the column oven was maintained at 25 °C. Ref: 10.1021/acs.analchem.7b00925, 10.1007/978-1-4939-7592-1_3
Meister zic-pHILIC pH9.3	HILIC	Merck SeQuant ZIC-pHILIC column	9.3	ACN:Water 5mM NH4Ac	5mM ammonium acetate in water	Polar metabolites were separated on a Agilent 1290 liquid chromatography system equipped with HILIC SeQuant ZIC-pHILIC (Merck, Darmstadt, Germany) column 100 Å (100 × 2.1 mm, 3.5 μm particle size) coupled to a guard column (2.1 × 2 mm, 3.5 μm particle size) and an inline-filter. Sample analysis was performed using 5mM ammonium acetate in water, pH = 9.3 (adjusted with 0.04% NH4OH) as solvent A and acetonitrile as solvent B. The elution gradient used was as follows: 88-60% B from 0 to 8.5 min, 60-25% from 8.5min to 11.2min, followed by isocratic wash step at 25% B from 8.7 to 11.2min, and reequilibration at 88% B from 11.5 to 22min. The flow rate was 0.28 mL/min; injection volume was 0.8 μL, and the column oven was maintained at 35 °C.
AjsTestF	HILIC	Waters Acquity UPLC-BEH Amide column	N/A	Water:MeOH	0.1% Formic Acid	Waters Acquity UPLC-BEH Amide column (150 mm x 2.1 mm; 1.7 μm) coupled to an Acquity UPLC BEH Amide VanGuard precolumn (5 x 2.1 mm2 ; 1.7 μm). The mobile phases consisted of (A) water with ammonium formate (10 mM) and formic acid (0.125%) and (B) acetonitrile:water (95:5, v/v) with ammonium formate (10 mM) and formic acid (0.125%). The separation was conducted under the following gradient: 0 min 100% B; 0−2 min 100% B; 2−7.7 min 70% B; 7.7−9.5 min 40% B; 9.5−10.25 min 30% B; 10.25−12.75 min 100% B; 12.75−17 min 100% B.1
IJM_TEST	HILIC	Merck SeQuant ZIC-pHILIC	Alkaline	Water:ACN	10mM ammonium acetate	N/A
IPB_Halle	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18	Acidic	Water:ACN	0.1% Formic Acid	Chromatographic separations were performed on an Acquity UPLC system (Waters®) equipped with a 100x1.0 mm, particle size 1.8 μm HSS T3 column (Waters®) and injection volume of 2.7 μL (full loop injection), applying a binary gradient of water (A) and acetonitrile (B), both acidified with 0.1 % FA with the following gradient program: 0 to 1 min, isocratic 95 % A, 5 % B; 1 to 16 min, linear from 5 to 95 % B; 16 to 18 min, isocratic 95 % B; and 18 to 20 min, isocratic 5 % B. Reference: 10.1007/s00216-013-6954-6
Mceachran HPLC #1	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18	6.5	Water:MeOH	0.1% Formic Acid	N/A
Cao_HILIC	HILIC	Merck SeQuant ZIC-pHILIC column	Acidic	ACN:Water	FA:ammonium formate	Plant sample preparation, extraction and experimental setups for the HILIC-MS were the same as those previously described (Fraser et al. 2012). Briefly, samples were extracted with 50:50 acetonitrile–water (v/v) and separated on a Merck polymeric bead based ZIC-pHILIC column (100 9 2.1 mm2 , 5 lm, zwitterionic stationary phase) using a mixture of acetonitrile-formic acid (solvent A) and water–ammonium formate (solvent B, pH 6.3) as the mobile phases. Chromatography was performed at 25 C with a gradient elution programme that held at 97 % A (0–1 min), 97–70 % A (1–12 min), 70–10 % A (12–14.5 min), 10 % A (14.5–17 min), returned to 97 % A (17–18.5 min) and allowed to equilibrate for a further 5.5 min prior to the next injection. Ref: 10.1007/s11306-014-0727-x

Chromatographic Method (CM) descriptions continued:

CM name	LC technique	Column	Temperature (°C)	Mobile phase	Sample matrix	Flow rate (mL/min)	Run time (min)	LC gradient (t[min], %B)
CS1	UHPLC: Thermo U3000 QTOF MS: Bruker Impact HD2	Waters Acquity HSS T3 (2.1x150 mm, 1.8 μm, 100 Å)	30	A: H2O + 0.1% FA B: ACN + 0.1% FA	Solvent, plasma	0.4	26	(0, 0), (2, 0), (15, 100), (22,100), (22.1, 0), (26, 0)
CS2	UHPLC: Agilent 1290 QTOF MS: Agilent 6540	Agilent Zorbax Eclipse XDB C18 (2.1x100 mm, 1.8 µm, 80 Å)	50	A: H2O +0.1% FA B: MeOH +0.1% FA	Plasma	0.4	16.5	(0, 2), (10, 100), (14.5, 100), (14.51, 2), (16.5, 2)
CS3	UHPLC: Thermo U3000 QTOF MS: Bruker Impact HD2	Waters Acquity UPLC BEH Shield RP18 (2.1x100 mm, 1.7 µm, 130 Å)	30	A: H2O +0.1% FA B: ACN +0.1% FA	Solvent, urine	0.6	26	(0, 0), (2, 0), (7, 10), (22, 95), (22.1, 0), (26, 0)
CS4	UHPLC: Agilent 1290 Infinity QTOF MS: Agilent 6550 iFunnel	Agilent Zorbax Eclipse Plus RRHD (2.1x50 mm, 1.8 µm,95 Å)	30	A: H2O +0.1% FA B: ACN +0.1% FA	Plasma, urine	0.4	12	(0, 1), (5, 10), (8, 25), (9.1, 99), (10, 99), (12, 1)
CS5	UHPLC: Thermo Accela 1250 QTRAP MS: Thermo Exactive	Agilent Zorbax Eclipse Plus RRHD (2.1x50 mm, 1.8 µm,95 Å)	30	A: H2O +0.1% FA B: ACN +0.1% FA	Plasma, urine	0.4	12	(0, 1), (5, 10), (8, 25), (9.1, 99), (10, 99), (12, 1)
CS6	HPLC: Agilent 1260 QTOF MS: Agilent 6530	Phenomenex Synergi Hydro- RP (2x150 mm, 4 µm, 80 Å)	30	A: H2O +0.1% FA B: ACN +0.1% FA	Solvent, urine	0.5	45	(0, 5), (1, 5), (35, 45), (40, 100), (45, 100)
CS7	UHPLC: H-class QTOF MS: Synapt G2 S	Waters Acquity UPLC BEH Shield RP18 (2.1x150 mm, 1.7 µm, 130 Å)	40	A: H2O +0.1% FA B: ACN +0.1% FA	Solvent, urine	0.4	37.1	(0, 5), (30, 50), (31, 100), (37, 100), (37.1, 0)
CS8	HPLC: Waters HPLC 2695 PDA: Waters 2996	Interchim Supelcosil LC-18 (4.6x250 mm, 5 µm,120 Å)	40	A: H2O +0.1% TFA B: ACN +0.1% TFA	Solvent	1	50	(0,5), (45, 35), (47, 75), (49, 35), (50, 5)
CS9	HPLC: Agilent 1200 QTRAP MS: AB Sciex 4000	Phenomenex Kinetex PFP (4.6x100 mm, 2.6 µm,100 Å)	35	A: H2O +0.1% TFA B: ACN +0.1% TFA	Solvent	1.5	32	(0, 1), (7, 7.5), (14, 7.6), (17, 10), (18.5, 12), (20, 12.5), (24, 30), (25, 90), (25.1, 1), (32, 1)
CS10	HPLC: Waters Alliance 2695 QTOF MS: Waters Premier	Waters Atlantis T3 (2.1x100 mm, 3 µm,100 Å)	40	A: H2O +0.1% TFA B: ACN +0.1% TFA	Solvent	0.3	25	(0, 10), (1, 10), (6, 40), (7, 50), (8, 50), (14, 70), (16, 80), (18, 80), (20, 10), (25, 10)
CS11	UHPLC: Agilent 1290 QTRAP MS: Sciex 6500	Phenomenex Luna Omega Polar C18 (2.1x100 mm, 1.6 µm, 100 Å)	40	A: H2O +0.5% FA B: ACN +0.5% FA	Solvent, urine	0.5	7	(0, 5), (3, 50), (3.1, 100), (5, 100), (5.1, 5), (7, 5)
CS12	UHPLC: Agilent 1290 QTRAP MS: Sciex 6500	Phenomenex Luna Omega Polar C18 (2.1x100 mm, 1.6 µm, 100 Å)	40	A: H2O +0.1% FA + 10 mM NH4COOH B: ACN	Solvent, urine	0.5	14	(0, 5), (8, 20), (10, 100), (12, 100), (12.1, 5), (14, 5)
CS13	HPLC: Agilent 1200 QTOF MS: Agilent G6530A	Phenomenex Luna C18 (4.6x150 mm, 3 µm, 100 Å)	25	A: H2O +0.1% FA B: ACN +0.1% FA	Solvent, urine	0.5	65	(0, 0), (30, 30), (35, 40), (50, 80), (52, 80), (60, 0), (65, 0)
CS14	HPLC: Agilent 1290 QTOF MS: Agilent 6550	Agilent Poroshell 120 EC C18 (3x100 mm, 2.7 µm, 120 Å)	25	A: H2O +0.1% FA B: ACN +0.1% FA	Solvent, urine	0.4	30	(0, 5), (10, 25), (20, 40), (24, 90), (25, 90), (26, 5), (30, 5)
CS15	HPLC: Eskigent nanoLC QTOF MS: Sciex TripleTOF 6600	Eksigent HALO C18 (0.5x50 mm, 2.7 µm, 90 Å)	35	A: H2O +0.1% FA B: ACN +0.1% FA	Solvent, urine	0.01	16	(0, 5), (12, 95), (14, 95), (16, 5)
CS16	HPLC: AB Sciex MicroLC 200 QTOF MS: AB Sciex 6500+	Eksigent HALO C18 (0.5x100 mm, 2.7 µm, 100 Å)	45	A: H2O +0.9% FA B: ACN +0.9% FA	Solvent, urine	0.015	5	(0, 1), (0.5, 1), (4, 95), (4.5, 1), (5, 1)
CS17	HPLC: Agilent 1290 QTOF MS: Agilent 6520	Phenomenex Synergi Hydro (2x250 mm, 4 µm, 80 Å)	25	A: H2O +0.1% FA B: ACN +0.1% FA	Solvent, urine	0.2	50.1	(0 , 0.5), (7, 0.5), (12, 12.5), (25, 16.3), (47, 35), (48, 65), (50, 65), (50.1, 0.5)
CS18	HPLC: Dionex Ultimate 3000 FT Orbitrap LTQ- XL MS: Thermo	Phenomenex Kinetex Core shell (2.1x150 mm, 2.6 µm, 100 Å)	40	A: H2O +0.1% FA B: ACN +0.1% FA	Plasma	0.35	15	(0, 0), (1, 0), (12.5, 100), (14, 100), (14.2, 0), (15, 0)
CS19	HPLC: Dionex Ultimate 3000 FT Orbitrap LTQ- XL MS: Thermo	Phenomenex Kinetex Core shell (2.1x150 mm, 2.6 µm, 100 Å)	40	A: H2O +0.1% FA B: ACN +0.1% FA	Urine	0.35	12	(0, 0), (1, 5), (7, 45), (8.5, 80), (10.5, 80), (11, 5), (12, 5)
CS20	HPLC: Shimadzu Prominence System PDA: SPD-M20A	Phenomenex Kinetex PFP (4.6x100 mm, 5 µm,100 Å)	45	A: H2O +0.1% TFA B: MeOH	Solvent	0.6	20	(0, 40), (20, 72), (21,40)
CS21	HPLC: Waters Alliance 2695 QqQ-MS: Micromass® Quattro Micro	LiChrospher®100 LiChroCART® (4x250 mm, 5 µm,100 Å)	35	A: H2O +0.5% FA B: ACN +0.5% FA	Solvent	0.3	135	(0, 5), (10, 5), (30, 15), (45, 20), (65, 20), (95, 54), (110, 63), (115, 5), (135, 5)
CS22	UHPLC: Waters Acquity QTOF MS: Waters Premier	Waters Acquity BEH C18 (2.1x100 mm, 1.7 µm, 130 Å)	65	A: H2O +0.1% FA B: 80% ACN + 20% Ac +0.1% FA	Solvent, plasma	0.4	6	(0, 0), (5, 100), (5.5, 0), (6, 0)
CS23	UHPLC: Waters Acquity QTOF MS: Waters Premier	Waters Acquity HSS T3 C18 (2.1x100 mm, 2.6 µm,100 Å)	50	A: H2O +0.1% FA B: 70% ACN + 30% MeOH + 0.1% FA	Solvent, plasma, urine	0.5 to 1.2	7	(0, 5), (1, 8), (2, 15), (3, 40), (4, 70), (4.5, 100), (5, 100), (6.4, 100), (6.6, 5), (6.8, 5), (7, 5)
CS24	UHPLC: Dionex Ultimate 3000 QqQ-MS: Thermo Fisher TSQ Vantage	Phenomenex Kinetex EVO C18 (2.1x100 mm, 2.6 µm,100 Å)	40	A: H2O +0.2% FA B: ACN +0.2% FA	Plasma, urine	0.4	12	(0, 5), (0.5, 5), (7, 95), (8, 95), (8.5, 5), (12, 5)