The LC–MS/MS instrument consisted of a binary ultra‐high‐performance liquid chromatography (UHPLC) system, with two LC‐30 AD pumps, a SIL30‐ACmp autosampler, a CTO‐20 AC column oven and a DGU‐20A5R degasser, all from Shimadzu. A triple quadrupole mass spectrometer, AB SCIEX quadrupole linear ion trap (QTRAP®5500, Ontario, Canada), was coupled to the LC system with a Turbo V™ TurboIonSpray® source and was equipped with an inlet valve. The LC system and mass spectrometer were controlled and data were collected using Analyst® software version 1.6.2 (Sciex, Ontario, Canada). Quantitative data processing was done using the MultiQuant™ software version 3.0.1 (Sciex, Ontario, Canada).
Multiquant software version 3
Manufactured by AB Sciex
Sourced in Germany, Canada
MultiQuant software version 3.0.2 is a data processing and quantitative analysis application developed by AB Sciex. The software's core function is to provide users with tools for the acquisition, processing, and analysis of mass spectrometry data.
Automatically generated - may contain errors
Lab products found in correlation
Analyst software version 1, by AB Sciex (4 mentions)
Cto 20ac column oven, by Shimadzu (2 mentions)
Sil30 acmp autosampler, by Shimadzu (1 mentions)
Lc 30ad pump, by Shimadzu (1 mentions)
Dgu 20a5r degasser, by Shimadzu (1 mentions)
Api 4000 triple quadrupole mass spectrometer, by AB Sciex (1 mentions)
Synergi polar rp, by Phenomenex (1 mentions)
Lc 20ab, by Shimadzu (1 mentions)
Cto 20ac, by AB Sciex (1 mentions)
Cbm 20a, by AB Sciex (1 mentions)
Analyst version 1, by AB Sciex (1 mentions)
Sil 20ac ht, by AB Sciex (1 mentions)
Lc 20ad hplc system, by Shimadzu (1 mentions)
Analyst 1, by AB Sciex (1 mentions)
Qtrap 5500, by AB Sciex (1 mentions)
Agilent 1200 lc system, by Agilent Technologies (1 mentions)
Ctc pal autosampler, by CTC Analytics (1 mentions)
Cbm 20a communications bus module, by Shimadzu (1 mentions)
Iondrive turbo 5 source, by AB Sciex (1 mentions)
Sil 30ac autosampler, by Shimadzu (1 mentions)
9 protocols using multiquant software version 3
1
LC-MS/MS Quantification Method Development
2
LC-MS/MS Analysis of Organic Compounds
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The LC-MS/MS system consisted of an HPLC apparatus (Shimadzu LC-20AB, SIL-20AC HT, CTO-20AC, CBM-20A, Duisburg, Germany) and an API 4000 triple quadrupole mass spectrometer (Sciex, Darmstadt, Germany). The substance-specific parameters used for multiple-reaction-monitoring (MRM) measurement are listed in Online Resource 2. The following source parameters were applied: ion spray voltage (ESI+), 5500 V; temperature, 550 °C; nebulizer gas, 50 psi; heating gas, 60 psi; curtain gas, 30 psi; and collision gas (nitrogen), level 9. A Synergi™ Polar-RP (150 × 2 mm, 4 μm; Phenomenex, Aschaffenburg, Germany) was used as an analytical column protected by a guard column. The binary linear gradient consisted of eluent A (deionized water containing 5 mmol/L ammonium formate, 0.1% formic acid) and eluent B (LC-MS-grade methanol, 5 mmol/L ammonium formate, 0.1% formic acid) with a flow rate of 0.4 mL/min: 0 min 10% B, 10 min 40% B, and 26 min 100% B. The column was equilibrated at starting conditions for 6 min prior to each run. Analyst (Version 1.6.2) and MultiQuant software (Version 3.0.1), both provided by Sciex (Darmstadt, Germany), were used for data acquisition and processing.
3
Simultaneous Quantification of Drugs in Maternal Urine
4
Quantitative Analysis of Analytes
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During sample pretreatment a vortexer (IKA ® -Werke GmbH & Co. KG, Staufen, Germany), centrifuges (5424 and 5810R, both from Eppendorf, Hamburg, Germany), an Evaporator ® (Liebsch Labortechnik, Bielefeld, Germany), a 16-fold vacuum manifold (Macherey-Nagel GmbH & Co. KG, Weilmünster, Germany) and manometer (Ashcroft Instruments, Baesweiler, Germany), glass pipettes for single use (Brand, Wertheim, Germany) and Chromabond C18 SPE-cartridges, 3 mL, 500 mg (Macherey-Nagel GmbH & Co. KG, Weilmünster, Germany) were used.
For the chromatographic separation, an Agilent 1200 LC system (Agilent Technologies, Waldbronn, Germany) consisting of a binary pump (G1312B), a thermostated column compartment (G1316B) and a CTC PAL autosampler (CTC Analytics, Zwingen, Switzerland) were employed. Mass spectrometric detection was performed using a hybrid quadrupole-ion trap tandem mass spectrometer, 5500 QTrap (Sciex, Darmstadt, Germany) equipped with an electrospray ion-source (ESI). Nitrogen in the required purity for the mass spectrometer was produced by the nitrogen generator NGM 11 S (cmc Instruments, Eschborn, Germany). Instrument was operated by the Analyst Software Version 1.6.2 (Sciex, Darmstadt, Germany).
Quantification of the analytes was carried out using Multiquant software version 3.0 (Sciex, Darmstadt, Germany).
For the chromatographic separation, an Agilent 1200 LC system (Agilent Technologies, Waldbronn, Germany) consisting of a binary pump (G1312B), a thermostated column compartment (G1316B) and a CTC PAL autosampler (CTC Analytics, Zwingen, Switzerland) were employed. Mass spectrometric detection was performed using a hybrid quadrupole-ion trap tandem mass spectrometer, 5500 QTrap (Sciex, Darmstadt, Germany) equipped with an electrospray ion-source (ESI). Nitrogen in the required purity for the mass spectrometer was produced by the nitrogen generator NGM 11 S (cmc Instruments, Eschborn, Germany). Instrument was operated by the Analyst Software Version 1.6.2 (Sciex, Darmstadt, Germany).
Quantification of the analytes was carried out using Multiquant software version 3.0 (Sciex, Darmstadt, Germany).
5
Automated LC-MS/MS Metabolomic Profiling
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LC-MS/MS analyses were carried out on a Shimadzu Nexera LC-30AD liquid chromatograph, consisting of a SIL-30AC auto sampler, CTO-20AC column oven and CBM-20A communications bus module (Shimadzu Corporation, Kyoto, Japan), coupled to a QTRAP 6500+ triple quad MS detector equipped with an IonDrive Turbo V Source ( Sciex; Warrington, Cheshire, UK). Data acquisition and evaluation were performed with the Analyst software version 1.7.1 and MultiQuant software version 3.0.3, respectively(Sciex; Warrington, Cheshire, UK). Automated SPE clean-up was performed using SPE-03 PromoChrom 8-Channel High Volume Automated SPE system (PromoChrom Technologies, Richmond, BC, Canada). Sample evaporation was carried out by TurboVap II (Biotage, Uppsala, Sweden). MicroCen MR Eppendorf centrifuge was obtained from Herolab GmbH (Wiesloch, Germany).
6
Multivariate Data Analysis Software
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Analyst software version 1.6.3 and MultiQuant software version 3.0.3 (Sciex, Darmstadt, Germany) were applied for data acquisition and evaluation. Furthermore, Microsoft Excel 2010 (Microsoft Co., Redmond, WA, USA) and custom software developed in Node.JS (Linux Foundation, San Francisco, CA, USA) were used for data processing.
7
Targeted Metabolite Quantification with Peak View and MultiQuant
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Targeted metabolomics data were processed using Peak View 2.1 and MultiQuant software version 3.0.2 (SCIEX). Chromatographic peaks of targeted metabolites were annotated using the extract ion chromatogram lists on the basis of high‐accuracy MS, MS/MS fragmentation, isotopic distribution, and retention time compared with an in‐house library of 635 metabolite standards (IROA Technologies, Bolton, MA). In addition to the IROA database, the fragmentation spectra of all peaks were searched through Metlin and HMDB. Each identified metabolite was quantified by integrating peak area using MultiQuant software. The quantitative analysis was based on the total peak areas of extracted ion chromatograms of feature ions.
8
Biogenic Amines Quantification in Microdialysate and Plasma
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The biogenic amines were analyzed in microdialysate and plasma samples of experiment on days 1 and 8 according to a previously described method.23 Samples were randomized and amino acids and amines were derivatized by an Accq‐tag derivatization strategy. Plasma samples (5 μL) were reduced with tris(2‐carboxyethyl)phosphine and deproteinated by MeOH. Microdialysate samples (30 μL) were only reduced with tris(2‐carboxyethyl)phosphine. The samples were dried under vacuum while centrifuged (9400 g, 10 minutes, room temperature), and reconstituted in borate buffer (pH 8.8) with 6‐aminoquinolyl‐N‐hydroxysuccinimidyl carbamate derivatization reagent. The reaction mixtures were injected (1 μL) into an ultraperformance liquid chromatography‐tandem MS system, consisting of an Agilent 1290 Infinity II LC system, an Accq‐Tag Ultra column, and a Sciex Qtrap 6500 MS. The peaks were assigned using Sciex MultiQuant software version 3.0.2, integrated, normalized for their internal standards, and corrected for background signal. Only compounds with a QC relative SD under 30% were reported to assure the quality of the data.
9
Untargeted Metabolomics Data Processing
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Data was processed during analysis using a previously established method22 (link). Briefly, untargeted metabolomics data was processed using Peak View 2.1 and MultiQuant software version 3.0.2 (SCIEX). The acquired mass data were analyzed using PeakView with XIC Manager 1.2.0 (Sciex, Framingham, MA) for peak picking, retention time correction, and peak alignment. Metabolite identities were assigned by matching accurate mass (error < 10 ppm), retention time (error < 10%), MS/MS fragmentation (library score > 70), and isotope distribution (error < 20%) with an in-house library consisting of IROA standards (IROA Technology, Bolton, MA) and other commercially available standards (650 total). In addition to the IROA database, the fragmentation spectra of all peaks were verified with data from Metlin and HMDB. Only one missing value was observed in the human samples, which was dropped after verification of the peak intensity below the limit of quantitation.
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