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9 protocols using caplc system

1

Peptide Identification by LC-MS/MS

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Peptides generated in both filtrate and supernatant were analyzed in a CapLC system (Waters Corporation, Milford, MA, USA) connected to a Finnigan LTQ mass spectrometer (Fisher Scientific, Maltham, MA, USA) with an ESI nanospray source. The desalted and lyophilized samples were dissolved in 0.1% formic acid (FA) aqueous solution, and then loaded into a homemade reverse phase (RP) separation column (75 µm i.d. × 10 cm). The column was packed with 5 µm C18 silica beads (Dr. Maisch HPLC GmbH, Germany). Gradient elution was generated using 0.1% FA in water as Solvent A and 0.1% FA in ACN as Solvent B. The separation was started at a flow rate of ~ 200 nL/min (after flow splitting) with 2% B for 20 minutes, followed by a linear gradient increase to 50% B during a period of 60 minutes. After that, 80% B for 20 minutes and 2% B for 30 minutes were used to wash and equilibrate the columns. Positive mode full MS scan was carried out within a mass range of 300–2000 m/z and MS/MS was operated in a data-dependent mode. Collision induced dissociation (CID) with 35% collision energy was used to activate fragmentation.
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2

LC-MS/MS Protein Identification Protocol

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SCX fractions were analyzed by LC MS/MS with a QTOF2 mass spectrometer equipped with a Cap LC system (Waters) as described [27 (link), 29 (link)–31 (link)]. Protein identification utilized MASSLYNX 4.1 software (Waters), the Mascot search engine (Matrix Science, version 2.4.1), and the human Uni-Prot/Swiss-Protein sequence database (October 2014, 20,196 total sequences). Database search parameters were restricted to three missed tryptic cleavage sites, a precursor ion mass tolerance of 25 ppm, a fragment ion mass tolerance of 0.3 Da and a false discovery rate of ≤ 1%. Fixed protein modifications included N-terminal and epsilon-Lys iTRAQ modifications and S-methyl-Cys. Variable protein modifications included Met oxidation, Asn and Gln deamidation and iTRAQ Tyr. A minimum Mascot ion score of 20 was used for accepting peptide MS/MS spectra. Two unique peptides per protein were required for all protein identifications.
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3

Peptide Separation and MS Analysis

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The resulting peptide mixture was subjected to the CapLC system (Waters, Milford, MA,) utilizing a capillary column (75 m i.d., 10 cm in length, C SUN, Taiwan) with a linear gradient from 5% to 50% acetonitrile containing 0.1% formic acid over 46 min. The separated peptides were on-line analyzed under positive survey scan mode on a nano-ESI Q-TOF (Micromass, UK) instrument as previously described 24 (link). The scan range was from m/z 400 to 1600 for MS and m/z 50 to 2000 for MS/MS. The raw data was processed into a text file format of PKL with MassLynx 4.0 (subtract 30%, smooth 3/2 Savitzky Golay and center three channels 80% centroid).
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4

Analysis of Recombinant Factor IX by Mass Spectrometry

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Transgenic FIX (157.5 μg) was reduced with 2 mM dithiothreitol (Sigma) at 56°C for 1 h and alkylated for 1.5 h at room temperature (in the dark) with 5 mM iodoacetamide (Sigma). The sample was diluted with 50 mM ammonium bicarbonate and then 2 μg of trypsin was added and incubated for 18 h at 37°C. After tryptic digestion, the sample was deglycosylated overnight at 37°C either with or without PNGase F. The peptide fragments were analyzed by HPLC (Waters, Milford, MA) with a reversed phase column (Biobasic-18, 5 μm, 300 Å, 4.6 mm × 250 mm, Thermo Electron). The eluted fractions were collected manually according to the absorbance at 214 nm. Collected samples were dried by SpeedVac and then subjected to analysis by the CapLC System (Waters) using a capillary column (75 μm i.d., 10 cm in length, MST, Taiwan) with a linear gradient of 30% to 80% acetonitrile containing 0.1% formic acid over 40 min. The separated peptides were online analyzed under positive survey scan mode on an ESI-Q-TOF (Micromass, Manchester, UK) instrument. All MS/MS spectra were processed using Mascot Distiller (Matrix Science, London, UK), and the resulting PKL files were searched using the Mascot search engine v2.2 (Matrix Science).
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5

QTOF LC–MS/MS Analysis of Peptides

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QTOF LC–MS/MS analysis of extracted peptides was performed as described earlier [14 (link)]. Briefly, the reconstituted peptide samples (1 μL) were loaded for efficient chromatographic separation on a CapLC-System (Waters, Milford, MA, USA). Peptides were injected for sequence analysis into Q-TOF Ultima Global (Micromass, Manchester, UK) mass spectrometer, equipped with a nanoflow ESI Z-spray source in positive ion mode. MS/MS raw data was generated with MassLynx (Micromass), which was converted to Peak list (pkl) files using ProteinLynx Global Server bioinformatics tool (PLUGS; v 2.2; Waters, Manchester, UK). pkl files were searched by MASCOT search engine against SwissProt data bases for peptide matching. Search criteria includes trypsin enzyme for digestion, mass tolerance of ± 0.5 Da and MS/MS tolerance ± 0.5 Da; allowance of up to one missed cleavage peptide and modification of carbamidomethylation and oxidation of methionine.
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6

MALDI-TOF-MS and CapLC-QTOF Analysis

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Mass spectra were acquired using matrix-assisted laser desorption ionization (MALDI) and time-of-flight (TOF) mass spectrometry (MALDI-TOF-MS) and a bidimensional capillary liquid chromatography (CapLC system, Waters, Manchester, UK) coupled to a tandem quadrupole oa-TOF hybrid mass spectrometer with a collision-induced dissociation (CID) hexapole cell (QTOF, Waters-Micromass, Manchester, UK) and a nano Z-spray source, both operated in positive ion mode. The TOF analyzer was operated in the reflectron mode.
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7

Positive-ion Electrospray Mass Spectrometry

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Positive-ion electrospray ionization mass spectrometry analysis was performed on a Micromass Q-TOF ultima global mass spectrometer (Waters) coupled to a Waters CapLC system. Mobile phases were A: 95% H 2 O containing 4.9% acetonitrile and 0.1% formic acid (FA), and B: 95% acetonitrile containing 4.9% H 2 O and 0.1% FA. The injector, loop, column and solvents were cooled to 2 °C to minimize back-exchange using a home-made low temperature box (50 × 50 × 50 cm) maintained at 2 (±0.2) °C by a refrigeration compressor. For mass spectrometry analysis, the desolvation temperature was 413 K and the source temperature was 353 K. Nitrogen was used as both cone gas and desolvation gas with a flow rate of 40 L h -1 and 400 L h -1 , respectively. The collision energy was set up to 10 eV. Global deuterium uptake spectra were acquired in the range of m/z 500-2500. Local deuterium uptake spectra were obtained in the range of m/z 400-1800. MassLynx (ver. 4.0) software was used for analysis and post data processing.
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8

PFOS Quantification in Blood and Eggs

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The concentrations of PFOS were measured using combined liquid chromatography-mass spectrometry using a CapLC system (Waters, USA) connected to a Quadrupole-LIT quadrupole mass spectrometer (Applied Biosystems, UK) as it was described in Dorneles et al. (2008) . Aliquots of 5 l were loaded on an Optiguard C18 pre-column (10 mm x 1 mm i.d., Alltech, USA). The analysis was performed on a Fluophase PFP column (50 mm x 1 mm i.d., Thermo, USA) at a flow rate of 40 l/min. The mobile phase was 2 mM NH4OAc (A) / Acetonitrile (B). A gradient elution was used starting at 35 % B and going to 90 % B in 5 min. At 5 min and 6 seconds the initial conditions were resumed. PFOS was measured under (-) electrospray ionisation using the transitions from mother to daughter ion (499 → 80/99) to identify them. The dwell time was 0.1 s. The ES-capillary voltage was set at -4.5 kV and the cone voltage -100 kV. The PFOS concentration was calculated using an un-extracted calibration curve. The limit of detection (LOD) was 0.9 ng/mL and 0.15 ng/g ww for blood and eggs respectively. This was established on a signal to noise ratio (S/N) > 3.
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9

Synthesis of Imidazo[1,2-a]pyridine Derivatives

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All reactions were carried out in oven dried 10 mL microwave vials. Other glassware (roundbottomed flasks) can be used but must be sealed tightly as gaseous products arise. All ketones and amines were purchased from commercial suppliers (Sigma-Aldrich, Acros Organics, Alfa-Aesar, Fluorochem, TCI and J&K). Calcium carbide was obtained from Sigma-Aldrich in granulated form (pieces) and technical quality (≥ 75% gasvolumetric). Calcium carbide is further ground in a mortar with a pestle until a fine powder is obtained and used immediately. 1 H ( 13 C) NMR spectra were recorded at 400 (100) MHz on a Bruker Avance III HD spectrometer using CDCl3 as solvent and TMS as the internal standard. Assignments were determined using 2D (HSQC, HMBC and DEPT or APT) spectra. Chemical shifts are given in parts per million (ppm), Jvalues are given in hertz (Hz), and number of protons for each signal are also indicated. For high resolution mass spectrometric analysis (HRMS), samples were dissolved in methanol/water (1/1), containing 0.1% formic acid and diluted to a concentration of approximately 10-6 mol/L. 10 µl of this solution was injected using a CapLC system (Waters) and electrosprayed using a standard electrospray source, positive ion mode accurate mass spectra were acquired using a Q-TOF II instrument (Waters). The parent ions [M+H]+ are quoted.
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