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4700 proteomics analyser

Manufactured by Thermo Fisher Scientific
Sourced in United States

The 4700 Proteomics Analyzer is a mass spectrometry instrument designed for the analysis of proteins. It features a time-of-flight (TOF) analyzer and a matrix-assisted laser desorption/ionization (MALDI) ion source. The instrument is capable of performing high-throughput analysis of protein samples.

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6 protocols using 4700 proteomics analyser

1

MALDI-ToF-MS Analysis of Enriched Fructans

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Enriched fructans oligosaccharides were analysed by MALDI-ToF-MS using a 4700 Proteomics Analyser (Applied Biosystems), as described by Maslen et al. [41 ]. The matrix was 2,5-dihydroxybenzoic acid (10 mg ml−1 dissolved in 50% MeOH). Three different T1 plants and three different T4 plants were used for this analysis. The MALDI-ToF-MS was done with three technical replicates. The results were statistically analyzed by Student’s t test.
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2

MALDI-ToF/ToF-MS/MS Analysis of Glycans

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Per-methylated samples were analysed by MALDI-ToF/ToF-MS/MS (4700 Proteomics Analyser, Applied Biosystems, Foster City, CA, USA) as previously described [50] (link), using 2,5-dihydroxybenzoic acid (2,5-DHB) matrix (10 mg ml−1 dissolved in 50% MeOH). The above tandem mass spectrometer uses a 200 Hz frequency triple Nd-YAG laser operating at 355 nm wavelength. High energy MALDI-CID spectra were acquired with an average 10,000 laser shots/spectrum, using a high collision energy (1 kV). The oligosaccharide ions were allowed to collide in the CID cell with argon at a pressure of 2×10−6 Torr.
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3

In-Gel Tryptic Digestion and MALDI-TOF-TOF MS

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The protein spots of interest were excised and de-stained with 25 mmol/l ammonium bicarbonate/50% acetonitrile (CAN), and in-gel digestion was performed with 0.01 µg/µl trypsin (Promega, Madison, Wisconsin, USA) in 25 mmol/l ammonium bicarbonate for 15 h at 37°C. The hydrolysates were collected, and the tryptic peptides were extracted from the gel pieces sequentially with 5% TFA at 40°C for 1 h and then 2.5% TFA/50% ACN at 30°C for 1 h. The extracts were pooled, lyophilized and stored at -20°C until use. Gel pieces from a 'blank' region and from the BSA molecular mass marker were used as negative and positive controls, respectively.
Subsequently, the peptide mixtures were re-dissolved in 0.5% TFA, and 1 µl of peptide solution was mixed with an equal volume of matrix (4-hydroxy-a-cyanocinnamic acid in 30% ACN/ 0.1% TFA). Then, the peptides were spotted on the target plate. Individual protein peptides were identified by MALDI-TOF-TOF mass spectrometry on a 4700 Proteomics Analyser (Applied Biosystems, Foster City, California, USA). The mass spectra were used to examine human protein sequences in the Swiss-Prot database using the Mascot database search algorithm (version 1.9).
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4

MALDI-ToF-MS/MS Analysis of Oligosaccharides

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Native or reductively aminated samples were analysed by MALDI-ToF-MS/MS (4700 Proteomics Analyser; Applied Biosystems, http://www.appliedbiosystems.com), as previously described (Maslen et al., 2007 (link)), using 2,5-dihydroxybenzoic acid (2,5-DHB) matrix (10 mg ml−1 dissolved in 50% MeOH). The above tandem mass spectrometer uses a 200-Hz frequency triple Nd-YAG laser operating with a wavelength of 355 nm. High-energy MALDI-CID spectra were acquired with an average of 10 000 laser shots/spectrum, using a high collision energy (1 kV). The oligosaccharide ions were allowed to collide in the CID cell with argon at a pressure of 2 × 10−6 Torr (0.27 mPa).
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5

Protein Identification via MALDI-TOF MS

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For the identification of the target protein, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used. Proteins were visualized with CBB-G250 after SDS-PAGE, and then the target bands were excised from the gel and washed with 25 mM NH HCO , 40 % (v/v) ethanol five times. The gel was cut into pieces and dehydrated with 1 ml of acetonitrile and dried in vacuo. Following this, 0.1 µg/ml trypsin in 25 mM NH HCO was added to the gel pieces and incubated at 37 °C for 16 h. Peptide fragments were extracted from the gel pieces with 50 % (v/v) acetonitrile, 5 % (v/v) trifluoroacetic acid for 30 min. The extracts were dried in vacuo, dissolved in 5 µl of 50 % (v/v) acetonitrile, 0.1 % (v/v) trifluoroacetic acid, and subjected to an ABI 4700 proteomics analyzer (Applied Biosystems). Mass fingerprints of tryptic peptides dissolved in 5 µl of 50 % (v/v) acetonitrile, 0.1 % (v/v) trifluoroacetic acid were generated by MALDI-TOF-MS using an Applied Biosystems 4700 Proteomics Analyser with TOF/TOF optics in the MS mode. A Nd:YAG laser (355 nm) was used to irradiate the sample. The spectra were acquired in reflection mode in the mass range 700-3200 Da. Amino-acid sequences of the fragments were determined in MS/MS mode with DeNovo Explorer software (Applied Biosystems).
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6

MALDI-TOF-MS Analysis of Glycans

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The isolated oligosaccharides were analysed by MALDI-TOF-MS. The matrix was a dihydroxybenzoic acid solution in 50% ACN (10 mg.ml -1 ). The analyses were carried on a 4700 Proteomics Analyser with TOF/TOF optics (Applied Biosystems, Framingham, MA). The mass spectrometer had a 200 Hz frequency-tripled Nd-YAG laser operating at a wavelength of 355 nm. A total of 1500 shots were acquired in the MS mode. Spectra from m/z 900 to 3000 were recorded. Glycans were detected as [M+Na] + ions.
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