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Lcq deca xp max

Manufactured by Thermo Fisher Scientific
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The LCQ Deca XP Max is a high-performance liquid chromatography-mass spectrometry (LC-MS) system designed for a wide range of analytical applications. It provides sensitive and reliable detection of a variety of analytes, including small molecules, peptides, and proteins. The system features a robust ion trap mass analyzer that delivers high mass accuracy and resolution.

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32 protocols using lcq deca xp max

1

Analytical HPLC for Peptide Purity

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Purity was determined by reversed-phase analytical HPLC (see Supplementary Figs 7–9) using a Phenomenex Gemini C18 column (100 × 4.6 mm), with 5 μm particle size and 110 Å pore size, connected to a HPLC system equipped with an autosampler (Shimadzu SIL-20A XR), degasser (Shimadzu DGU-20A3) and a high-pressure gradient system comprising two LC-20AD XR pumps (Shimadzu). Separation was performed at a flow of 1 ml min−1 and using a 20-60% acetonitrile linear gradient in water containing 0.1% NH4OH. All eluents and additives were HPLC grade. Peptides, cyanine dye-coupled peptides and eventual contaminants were detected using a PDA (Shimadzu SPD-M20A), acquiring a full ultraviolet-visible spectrum between 200 and 750 nm at any time point. Main chromatogram peaks were collected and product mass confirmed by ESI mass spectrometry using a LCQ Deca XP Max (Thermo Finnigan) ion-trap mass spectrometer. For that, samples were manually injected bypassing the column at a flow rate of 0.20 ml min−1 and positive ion mass spectra were acquired in standard enhanced mode.
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2

Quantitative AHL Analysis via HPLC-MS

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High performance liquid chromatography mass spectrometry was used to analyze AHL production by YZ1 and YZ2 using a LCQ Deca XP max (Thermo Finnigan, USA; Yin et al., 2012 (link); Chen et al., 2013 (link)). Liquid chromatography steps utilized a C18 column of 4.6 × 150 mm, 5 μm particle size, with injection volume of 20 μl and a flow rate of 0.3 ml/min. Mobile phases were 0.1% v/v formic acid in water and 0.1% v/v formic acid in acetonitrile, respectively. Mass spectrometry was run in ESI-positive mode, with probe capillary voltage set at 3,000 V, a desolvation temperature of 350°C, sheath gas of 11 ml/h, and a nebulizer pressure of 50 psi (Chen et al., 2013 (link)).
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3

Profiling Cellular Fatty Acids and Lipids

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The cellular fatty acids of strains JW1T, JW3, and the reference strains were determined under identical conditions in parallel. The quadrant streak method was used for inoculation and cellular fatty-acid methyl esters were obtained from cells grown on MA at 30°C for 16 h from quadrant 3 (late exponential phase). Whole cell fatty acids were analyzed using the Microbial Identification System (MIDI Inc.) according to the manufacturer’s instructions. Isoprenoid quinones were extracted and purified by two-dimensional thin-layer chromatography (TLC) and then analyzed by LC-MS (Agilent 1200 and Thermo Finnigan LCQ DECA XP MAX mass spectrometer) [34 ]. Total lipids were extracted and separated by two-dimensional TLC [35 ] on silica gel 60 F254 plates (Merck). Four types of spray reagent were used to detect the corresponding lipids, including molybdophosphoric acid for total lipids, α-naphthol reagent for glycolipids, ninhydrin reagent for lipids containing free aminolipids, and molybdenum blue for phosphorus-containing lipids [36 (link)].
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4

LC-MS Analysis of Phosphopantetheinylated E. coli Products

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The ACPs produced from E. coli or from the phosphopantetheinylation reaction mixture were directly analyzed by LC-MS (Agilent 1200, Thermo Finnigan LCQ Deca XP MAX). LC separation was carried out on a Agilent SB-C18 column (3.5 μm, 80 Å, 2.1 × 150 mm, Agilent) at 35 °C. Solvent A consisted of 0.1% formic acid. Solvent B consisted of acetonitrile. The following binary gradient was used: 0–5 min, 5% B; 5–45 min, a linear gradient to 75% B; followed by 3 min isocratic elution of 75% B, and equilibrated to initial condition for 13 min at a flow rate of 0.2 ml/min. UV detection was performed at both 254 nm and 280 nm. MS equipped with ESI source was performed as follows: positive; source voltage, 2.5 kV; capillary voltage, 41 V; sheath gas flow, 45 arb; aux/sweep gas flow, 5 arb; capillary temperature, 330 °C.
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5

Synthesis of Cortisol-3-CMO-Maleimide Probe

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Ten mg hydrocortisone
3-(O-carboxymethyl)oxime (Toronto Research Chemicals) and 10.4 mg
2-(7-Aza-1H-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate
(HATU, Fluorochem) were dissolved in 2 mL DMF. Subsequently, 44 μL
diisopropylethylamine (DIPEA, Sigma) was added together with 16.5
mg 1-(2 aminoethyl)maleimide hydrochloride (Sigma) before the mixture
was stirred for 4 h at room temperature. DMF was removed using a Buchi
rotary evaporator and a diaphragm pump. The remaining compound was
dissolved in Milli-Q water with 25% HPLC-grade acetonitrile and 0.1%
formic acid. Cortisol-3-CMO-maleimide was purified with a preparative
LC-MS system comprising of an LCQ Deca XP Max (Thermo Finnigan) ion-trap
mass spectrometer equipped with a Surveyor photodiode detector array
(PDA) detector (Thermo Finnigan). The mixture was purified with a
Phenomex kinetex 2.6 μm EVO C18 50 × 2.1 mm column and
an isocratic acetonitrile gradient of 34%. Fractions with the correct
mass (E/Z isomers were not separated) were collected using a PrepFC
fraction collector (Gilson Inc.) and subsequently freeze-dried before
being dissolved in DMSO and stored at −30 °C (Figure S4).
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6

ESI-MS Analysis of Peptides and Proteins

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The ESI mass spectrum data of small peptides and proteins were obtained from a Thermo Finnigan LCQ DECA XP MAX (ESI ion source, positive mode). MagTran 1.03 and ESIProt 1.0 software were used for data deconvolution.
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7

HPLC-MS/MS Metabolite Analysis

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The metabolites were separated by an HPLC system (Thermo Finnigan, Waltham, MA, USA) using 0.1% (V/V) formic acid in water (buffer A) and 100% acetonitrile (buffer B) as mobile phases at a flow rate of 0.15 ml/min. The HPLC separation was carried out using a reversed-phase column (ZORBAX 300SB-C18, 2.1 × 150 mm, 3.5 μm; Agilent, Santa Clara, CA, USA). The gradient profile was 8% B for 2 min, increased to 20% B in 38 min, then to 100% B in 12 min and maintained for 10 min, and decreased to 8% B in 2 min and maintained for 10 min. The acquisition time was 55 min and delay time was 5 min per spectrum. The metabolites were detected by monitoring the absorption at 280 and 340 nm.
The metabolites were identified using an ion trap mass spectrometer (LCQ DECA XP MAX) coupled with an ESI source (Thermo Finnigan). The MS parameters for analysis were: capillary temperature 280 °C, spray voltage 4.5 kV, sheath gas (nitrogen) flow rate 40 arb and aux/sweep gas (nitrogen) flow rate 10 arb. Collision energy and other tune parameters were optimized for dissociation of parent ions into product ions for each metabolite. The mass spectrometer was acquired in data-dependent MS/MS mode: each full MS scan (in the range 100–220 m/z) was followed by four MS/MS of selected ions including substrate, intermediate product, end product and internal standard.
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8

Shotgun Proteomics with LC-MS/MS

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Samples were loaded on a self-packed fused silica (Polymicro Technologies) trap column (360 micron o.d. × 100 micron i.d.) with a Kasil frit packed with 5–15 micron irregular phenyl C-18 YMC packing. The trap column was connected to an analytical column (360 micron o.d. × 50 micron i.d.) with a fritted tip at 5 micron or less (New Objective) packed with 5um phenyl C-18 YMC packing. Peptides were trapped and then eluted into a Thermo Finnigan LCQ deca XP max mass spectrometer with an acetonitrile gradient from 0 % to 80 % over one hour at a flow rate of between 50–150 nl/minute. The mass spectrometer was operated in data dependent mode. First a MS scan from mass 200 or 300–2000 m/z was collected to determine the mass of molecules eluting at that time, the top two most abundant masses were fragmented into MS/MS scans and placed on an exclusion list. This sequence MS followed by 2 MS/MS scans with exclusion was repeated throughout the 15 minute gradient. Ion chromatograms were plotted of the masses of interest.
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9

Identification of Phenolic Compounds by ESI-ITMS

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Identification of phenolic compounds present in the different HPLC separated fractions was carried out by ESI-ITMSn using a Finnigan LCQ DECA XP Max ion trap mass spectrometer (Thermo Finnigan, San Josè, CA, USA), equipped with Xcalibur® system manager data acquisition software (Thermo Finnigan, San José, CA, USA). Mass spectra were recorded from mass-to-charge ratio (m/z) 80 to 1800 both in negative and in positive ionization mode. The capillary voltage was set at −28 V, the spray voltage was at 3 kV and the tube lens offset was at −10 V in negative ion mode, while the capillary voltage was set at 34 V, the spray voltage was at 3.5 kV and the tube lens offset was at 55 V in positive ion mode. The capillary temperature was 275 °C. Data were acquired in MS, MS/MS and MSn scanning mode.
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10

Ovary Cholesterol Quantification Protocol

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Ovaries were weighted and put into a tube with 1ml chloroform-methanol (2:1, V/V) solution. After thoroughly homogenized, the substances were removed by centrifugation and the fluid was dried using nitrogen gas (N2). To get total cholesterol, 1U cholesterol esterase (Worthington) were added and the reaction was proceeded at 37°C for 1 hour. 1ml hexane was used to extract the total lipid. The hexane phase was dried and re-dissolved in 50μl acrylonitrile- isopropanol (4:1). 20μl fluid was used to detect total cholesterol content. Standard curve were done by accurate weighting and gradient diluting the standard cholesterol (Sigma). All of the HPLC analyses used an Agilent 1200 system. The reactions were analyzed using an Agilent Extend-C18 column (5um, 4.6×250mm) thermostatted at 35°C, a solvent system of methanol: Acetonitrile (9:1, v/v) and a flow rate of 0.8ml/min. The mass detection was carried out by a Thermo Finnigan LCQ Deca XP MAX. The source type was Atmospheric Pressure Chemical Ionization (APCI) in positive polarity mode. The capillary temperature and APCI vaporizer temperature was 150°C and 450°C respectively.
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