Experimental data for study Local Asymmetric Gaussian Fitting (LAGF) Algorithm for Enhanced Peak Detection of Liquid Chromatography-High Resolution Mass Spectrometry Data

TCSP was a LC-MS data file of a mixture of 16 organophosphate ester (OPE) standards, which was a part of the study of OPEs-ID . And the experimental procedure for TCSP was as follows. An ultra-performance liquid chromatography (UPLC) coupled to an Orbitrap Exploris™ 240 Mass Spectrometer spectrometry system (HRMS) with heated electrospray ionization mode (H-ESI) in positive was used (Thermo Fisher, USA). The ACQUITY UPLC BEH Shield RP18 130 Å column (50 mm × 2.1 mm; 1.7 µm particle size; Waters, Milford, U.S.) with a pre-column (ACQUITY UPLC BEH Shield RP18, 130 Å, 1.7 µm, 2.1 mm × 5 mm Waters, Milford, U.S.) was used for the chromatographic separation at a flow rate of 0.3 mL/min. The mobile phase consisted of water containing 0.1% formic acid (A) and methanol (B). The gradient started with 5% B for the first 2 min; linearly ramped to 40% B in 4 min then to 60% B in 6 min, and a linear increase to 100% B in 10 min and held for 5 min; followed by a linear decrease to 5% B in 0.1 min and held for 5 min. The spray voltages of H-ESI were set to + 3500 V. The vaporizer temperature was set as 350 ℃ and the flow rates for sheath gas, auxiliary gas and sweep gas were set to 40, 10 and 1 (arbitrary units), respectively. The full scan and an iterative data-dependent acquisition (DDA) strategy using the AcquireX Deep Scan workflow were applied. The scan range of full scan mode was set as m/z 100–1200.

PFST was a LC-MS data file of per- and polyfluoroalkyl substances (PFAS), which included a mixture of 44 PFAS standards. The mixture of PFAS standards was dissolved in methanol. A Thermo Scientific Ultimate 3000 UHPLC coupled with a mass spectrometer Q-Exactive plus (Thermo Fisher Scientific, USA) was used for LC-MS analysis of PFAS. All samples were analyzed with an Acquity UPLC BEH C18 column (2.1 mm x 100 mm, 1.7 μm, Waters) at 45℃. Mobile phase A was an aqueous solution of 10 mM ammonium formate, while mobile phase B was pure acetonitrile. The gradient started with 5% B for 1 min; linearly ramped to 90% B in 11 min, and linearly increased to 100% B in 4 min; followed by a linear decrease to 5% B in 0.5 min and held for 4 min. The spray voltage of ESI was set to + 3200 V. The vaporizer temperature was set as 350 ℃ and the flow rates for sheath gas and auxiliary gas were set to 45 and 10 (arbitrary units), respectively. All MS data were collected in ESI negative ion mode within the range of m/z 100-1000. The injection volume was 1 mL.

LMT01 was a LC-MS data file of a pooled human serum lipid sample, which was extracted by methyl tert-butyl ether (MTBE) method. The extraction method was as follows: human serum stored at -80 ℃ was thawed in a refrigerator at 4 ℃. 20 μL of serum was taken out and 15 μL of 25 g/mL TG 51:0 was added as internal standard. 150 μL of cold methanol solution was added and vortexed for 10 s. Subsequently, 500 μL of MTBE was added and vortexed for 10 s. Then the mixture was placed in a 15 ℃ incubator and shaken at 450 rpm for 15 min. 150 μL of deionized water was added into the turbid solution and vortexed for 10 s. The mixed solution was equilibrated at 4 ℃ for 10 min, then centrifuged at 8000 rpm for 10 min. 200 μL of the supernatant was dried in a vacuum concentrator and stored in a -80 ℃ refrigerator. Prior to LC-MS analysis, 100 μL of ACN: IPA: H₂O = 60:35:5 (v/v/v) solvent mixture was added for re-solubilization.

A Thermo Scientific Ultimate 3000 UHPLC coupled with a mass spectrometer Q-Exactive plus (Thermo Fisher Scientific, USA) was used for LC-MS analysis of lipids. All samples were analyzed with a Xtimate UHPLC C18 column (2.1 × 100 mm, granulation of 1.8 μm, Welch, China) which was maintained at 60 °C and eluted with a multistep gradient over the course of 15 min at a 0.25 mL/min flow rate. The mobile phases A and B were ACN/H2O=6:4(v/v), IPA/ACN=9:1(v/v), both containing 10 mM ammonium acetate. The gradient started with 35% B for 1 min; linearly ramped to 85% B in 8 min then increased to 97% B within 0.5 min, and held for 3.5 min; followed by a linear decrease to 35% B in 0.5 min and held for 1.5 min. The injection volume was 1 mL.

AAM was a LC-MS data file of amino acids (AAs), which included a mixture of 19 AA standards. The mixture of standards was dissolved in methanol. An Ultimate 3000 UHPLC coupled with a mass spectrometer Q-Exactive plus (Thermo Fisher Scientific, USA) was used for LC-MS analysis of AAs. All samples were analyzed with an ‌ACQUITY UPLC Glycan BEH Amide column (2.1 mm x 100 mm, 1.7 μm) under HILIC separation mode at 40℃. Mobile phase A was an aqueous solution containing 20 mM ammonium formate and 0.35% formic acid, while mobile phase B was a mixed solution of acetonitrile and water (acetonitrile: water = 9:1) containing 20 mM ammonium formate and 1.15% formic acid. The gradient started with 5% A for 2 min; linearly ramped to 20% A in 5 min, and a linear increase to 40% A in 3 min and held for 2 min; followed by a linear decrease to 5% A in 0.1 min and held for 2.9 min. The injection volume was 1 mL. The mass spectrometry scanning mode was positive ion mode, and the scanning range was m/z 50-500.

TSQ series data were data files of a series of seven organophosphate esters (OPEs) (triethyl phosphate, tributyl phosphate, tris(2-chloroethyl) phosphate, tripropyl phosphate, tris(1-chloro-2-propyl) phosphate, Tris(1,3-dichloro-2-propyl) phosphate and tris(2-ethylhexyl) phosphate) with the concentration of 100 ng/mL, 50 ng/mL, 20 ng/ml, 10 ng/mL, 5 ng/mL, and 1 ng/mL for each in methanol. LC-MS data of each concentration was acquired three times to obtain relative standard deviations for each analyte.

The data were obtained with an Ultimate 3000 UHPLC coupled with a mass spectrometer Q-Exactive plus (Thermo Fisher Scientific, USA). OPEs were separated on an ACQUITY UPLC BEH C18 column (2.1 mm × 100 mm, 1.7 μm, Waters, USA) using a reverse-phase chromatography method at 45°C. All MS data were collected in ESI positive ion mode within the range of m/z 100-1000. The flow rate was 0.30 mL/min. Mobile phase A was ultrapure water containing 0.1% formic acid, while mobile phase B was methanol. The gradient started with 5% B for the first 2 min; linearly ramped to 40% B in 2 min then to 60% B in 2 min, and a linear increase to 100% B in 2 min and held for 5 min; followed by a linear decrease to 5% B in 0.1 min and held for 2 min. The injection volume was 1 mL.

AAQ series data were data files of a mixture of eight amino acids (arginine, glutamic acid, histidine, lysine, phenylalanine, serine, threonine, and tryptophan) with the concentration of 5000 ng/mL, 2500 ng/mL, 1000 ng/ml, 500 ng/mL, 250 ng/mL, and 50 ng/mL for each in aqueous solutions containing 0.1% formic acid. The experimental procedure was as same as AAM dataset. LC-MS data of each concentration was acquired three times to obtain relative standard deviations for each analyte.

The SEUS series data were LC-MS data of 3-nitrophenylhydrazine (3-NPH)-derivatized serum samples. They were prepared by sequentially transferring 50 μL serum to a centrifuge tube, adding 100 μL methanol (vortexed 30 s), diluting with 300 μL ultrapure water, and centrifuging (10,000 rpm, 4°C, 5 min). A 50 μL aliquot of the supernatant was mixed with 20 μL 1-(3-Dimethylaminopropyl)-3-ethylcarbodiimide (EDC)-6% pyridine solution and 20 μL 3-NPH for a 1 h derivatization at room temperature, quenched with 400 μL methanol, recentrifuged, and the final supernatant was collected for LC-MS analysis. 

A Thermo Scientific Ultimate 3000 UHPLC coupled with a mass spectrometer Q-Exactive plus (Thermo Fisher Scientific, USA) was used for LC-MS analysis of derived serum samples. Separation was achieved on a Xtimate UHPLC C18 column (2.1 × 100 mm, 1.8 μm particle size; Welch, China) maintained at 40°C. The mobile phase consisted of (A) 0.1% formic acid in water and (B) acetonitrile-isopropanol (7:3, v/v), delivered at 0.4 mL/min via a 20-min stepwise gradient: 5% B (0–1 min), 5-30% B (1–5 min), 30-50% B (5–9 min), 50-80% B (9–12 min), 80-100% B (12–15 min), 100% B (15–18 min), 100-5% B (18–18.1 min), and 5% B (18.1–20 min). MS detection employed negative ion mode with a scan range of m/z 100–1000 and a 1 μL injection volume.