Transmission electron microscopy (TEM) (Hitachi H-8100) was used to characterize the surface morphology of CNPs and GNs. Raman spectra were measured with a SENTERRA dispersive Raman microscope spectrometer (Bruker Optics). A SHIMADZU UV-1800 spectrophotometer was used for UV-Vis measurements. MALDI-TOF-MS analyses were carried out using a 4800 MALDI TOF/TOF analyzer (AB SCIEX) equipped with a pulsed Nd:YAG laser at an excitation wavelength of 355 nm. For each MS spectrum 1250 laser shots were fired (50 sub-spectra, 25 shots per sub-spectrum). The mass spectra analyzed using Data Explorer 4.9 software (AB SCIEX). GlycoWorkbench software was employed for MS data interpretation.
Data explorer 4
Manufactured by AB Sciex
Sourced in Canada
Data Explorer 4.9 is a software application developed by AB Sciex for data analysis. The software's core function is to provide users with tools to visualize, process, and analyze data generated from various analytical instruments.
Automatically generated - may contain errors
Lab products found in correlation
4800 maldi tof tof analyzer, by AB Sciex (3 mentions)
H 8100, by Hitachi (2 mentions)
Uv 1800 spectrophotometer, by Shimadzu (2 mentions)
Senterra dispersive raman microscope spectrometer, by Bruker (1 mentions)
4800 maldi tof tof, by AB Sciex (1 mentions)
Ultima 3, by Rigaku (1 mentions)
5800 mass spectrometer, by AB Sciex (1 mentions)
Ziptip, by Merck Group (1 mentions)
4800 proteomics analyzer, by AB Sciex (1 mentions)
11 protocols using data explorer 4
1
Characterization of Carbon and Gold Nanoparticles
2
Characterization of Iron Oxide Nanoparticles
3
Determining Protein Molecular Weight by MALDI-TOF
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The molecular weight of purified proteins and deglycosylated proteins were determined using a 4800 MALDI TOF/TOF analyzer (AB SCIEX) equipped with a pulsed Nd: YAG laser at an excitation wavelength of 355 nm. One thousand two hundred fifty laser shots were fired (50 sub-spectra, 25 shots per sub-spectrum) for each MS spectrum. MALDI-spectra were recorded in positive-ion mode. Laser intensity was set to 4000 to 5000. The mass spectra were analyzed using Data Explorer 4.9 software (AB SCIEX). Samples were spotted and mixed with an equal volume of the sample and sinapinic acid matrix on a MALDI plate. Sinapinic acid was dissolved in 50% ACN/49.9% water/0.1% TFA at a concentration of 50 mM as the MALDI matrix.
4
MALDI-TOF-MS Analysis of Permethylated Glycans
5
MALDI-TOF Analysis of Permethylated Glycans
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Permethylated samples were dissolved in 10 μL of 50% methanol in water, 1 μL was mixed with 1 μL of 2,5-dihydroxybenzoic acid (10 mg/mL in 50% methanol in water). MALDI data were acquired in the positive ion reflector mode using a 5800 mass spectrometer (AB Sciex, Framingham MA). The MALDI data were analyzed using Data Explorer 4.9 (AB Sciex). The processed spectra were subjected to manual assignment and annotation with the aid of GlycoWorkBench (Ceroni et al. 2008 (link)). The proposed assignments for the selected peaks were based on composition together with knowledge of the biosynthetic pathways. Proposed structures were further confirmed by MS/MS analysis.
6
MALDI-TOF/TOF Mass Spectrometry Protocol
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Mass spectrometry experiments were performed using a 4800 MALDI TOF/TOF™ Analyzer
mass spectrometer (AB Sciex, Les Ulis, France). The samples were irradiated with
an Nd:YAG laser operating at 355 nm wavelength, producing 3 ns wide pulses. The
instrument was externally calibrated using a peptide mixture (peptide
calibration 1 and 2 from ABSciex between 700 and 3700 Da). Acquisitions were
performed in positive reflection mode. For the dried-droplet sample preparation
method, 0.5 µL of the sample was mixed with 0.5 µL of a solution of 4 mg/ml of
HCCA. For MS/MS experiments, precursor ions were accelerated at 8 keV, and the
MS/MS spectra were acquired using 2 keV collision energy, with CID gas at a
pressure of 3.5x10-6 Torr. Mass spectra were analyzed using Data
Explorer 4.9 (AB Sciex). For peptide sequence analysis, the mass tolerance of
the precursor was 10 ppm and 0.05 Da for fragment identification.
mass spectrometer (AB Sciex, Les Ulis, France). The samples were irradiated with
an Nd:YAG laser operating at 355 nm wavelength, producing 3 ns wide pulses. The
instrument was externally calibrated using a peptide mixture (peptide
calibration 1 and 2 from ABSciex between 700 and 3700 Da). Acquisitions were
performed in positive reflection mode. For the dried-droplet sample preparation
method, 0.5 µL of the sample was mixed with 0.5 µL of a solution of 4 mg/ml of
HCCA. For MS/MS experiments, precursor ions were accelerated at 8 keV, and the
MS/MS spectra were acquired using 2 keV collision energy, with CID gas at a
pressure of 3.5x10-6 Torr. Mass spectra were analyzed using Data
Explorer 4.9 (AB Sciex). For peptide sequence analysis, the mass tolerance of
the precursor was 10 ppm and 0.05 Da for fragment identification.
7
MALDI-TOF-TOF Analysis of N-Glycans
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This analysis of H11 was conducted using an established protocol (31 (link)). N-glycans were released from glycopeptides by PNGase F. PNGase F-resistant N-glycans were subjected to PNGase A digestion. Following porous graphitic carbon (PGC) purification (32 (link)), native glycans were permethylated by adding 100 μL of DMSO-NaOH slurry. Subsequently, the glycan sample was mixed with freshly-prepared 2,5-dihydroxybenzoic acid (DHB) before crystallisation at room temperature. N-glycome spectra were obtained in the positive ionisation mode using an AB 5800 MALDI-TOF-TOF instrument (SCIEX, Concord, Canada). The data were processed using Data Explorer 4.0 (SCIEX) and GlycoWorkbench (v.2.1).
8
MALDI-MS Analysis of Permethylated Glycans
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Spectra were obtained using the 5800 MALDI-MS instruments in the positive ionization mode (SCIEX, Concord, Canada). The dried glycan residues were reconstituted in 15 μL methanol solution. The matrix was prepared with 10 mg/mL DHB in 50% acetonitrile and 10 mM sodium acetate. 1 μL of permethylated glycan was mixed with 1 μL of freshly-prepared DHB before spotting on a MALDI-target plate and allowed to crystalize at room temperature. In total, 1000 laser shots were applied on each sample spot. MS/MS analyses were performed with air as CID gas using 2 kV collision energy. The final data were processed by DataExplorer 4.0 (SCIEX, Concord, Canada), and the selected spectra were annotated using GlycoWorkbench (2.1 build 146).
9
Peptide Sample Analysis by MALDI-TOF MS
10
Mass Spectrometry and Computational Chemistry
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DataExplorer 4.0 (AB Sciex, Darmstadt, Germany) was used to control data acquisitions and initial elaboration; SigmaPlot 14.5 was used to graph final mass spectra. ChemDraw Pro 8.0.3 (CambridgeSoft Corporation, Cambridge, MA, USA) was employed to draw chemical structures. Visualization and initial building were done by using ChemDraw Pro 10.0 and Chem3D Ultra 10.0. Initial geometries of the neutral and protonated compounds were created and optimized energetically by density functional theory (DFT) calculations. For proton affinity, DFTB3, based on a third-order expansion of the DFT total energy around a reference density, was used.
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