MALDI-TOF-MS spectra of DNA oligomers were measured using BRUKER ultraflex III. DNA oligomers were mixed with HPA (3-Hydroxy picolinic acid) (0.5 μM; 10 mg/ml)/DAC (Diammonium citrate) (0.5 μM; 1 mg/ml) matrix, which were applied to anchor chip followed by ionization using 60–70% laser irradiation.
Ultraflex 3
Manufactured by Bruker
Sourced in Germany, United States
The Ultraflex III is a high-performance MALDI-TOF/TOF mass spectrometer designed for advanced proteomics and biomolecular analysis. It provides high mass resolution, sensitivity, and accurate mass measurement capabilities.
Automatically generated - may contain errors
Lab products found in correlation
Flexanalysis 3, by Bruker (6 mentions)
Flexanalysis software, by Bruker (5 mentions)
C18 ziptip, by Merck Group (3 mentions)
Flexanalysis, by Bruker (3 mentions)
Scout mtp 384 target plate, by Bruker (3 mentions)
Modified porcine trypsin, by Promega (2 mentions)
Mascot 2.2 search engine, by Matrix Science (2 mentions)
Chemi lumi one, by Nacalai Tesque (2 mentions)
Ecl prime, by GE Healthcare (2 mentions)
Las 4000, by Fujifilm (2 mentions)
Ultraflextreme, by Bruker (2 mentions)
Autoflex 3, by Bruker (2 mentions)
Evoq gc tq, by Bruker (2 mentions)
1100 series, by Agilent Technologies (2 mentions)
Mascot version 2, by Matrix Science (2 mentions)
Pdquest 8, by Bio-Rad (1 mentions)
Biotools 3, by Bruker (1 mentions)
Mascot software, by Matrix Science (1 mentions)
Binary 1525, by Waters Corporation (1 mentions)
Maldi tof ms, by Bruker (1 mentions)
79 protocols using ultraflex 3
1
MALDI-TOF-MS Analysis of DNA Oligomers
2
MALDI-TOF Mass Spectrometry of Trypan Blue-Lutein/Zeaxanthin
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
MALDI-TOF mass spectra were recorded in a mass range of 200–5000 Da on an Ultraflex III mass spectrometer (Bruker Daltonics, Bremen, Germany) equipped with a Smartbeam laser and a LIFT-MS/MS facility. Each spectrum resulted from 3000 laser shots. The system was calibrated using a dextran ladder, as shown in S1 Fig . The trypan blue—lutein/zeaxanthin solutions (0.5 μl) were mixed on the ground steel target in a 1:1 ratio with the matrix consisting of 2,5-dihydroxybenzoic acid (10 mg/ml) dissolved in 10% aqueous acetonitrile. Baseline corrections and peak picking were performed using FlexAnalysis software version 3.0.9 (Bruker Daltonics, Bremen, Germany).
3
MALDI-TOF/TOF Proteomic Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Trypsin digested 2 DE spots samples were first desalted and concentrated on C18 Zip Tips (Millipore, USA). Desalted peptides samples were mixed with α-cyano-4-hydroxy cinnamic acid matrix in 1:1 ratio and the 2μl of this mixture was spotted on to the MALDI plate. The plate was analyzed on MALDI TOF/TOF Bruker Daltonics UltraFlex III instrument operated in positive-ion reflector mode of 500–3000m/z detection range. Further analysis was done with Flex AnalysisTM software (Bruker-Daltonics) and calibrated internally for autoproteolysis of peptides with trypsin to obtain the peptide mass fingerprint. Peaklist data files obtained were analyzed using peptide mass fingerprinting (MatrixScience) search against most recent mosquito database from UniProt for identification of the proteins. Parameters used for search were: fixed modification (carbamidomethyl), variable modification (Methionine oxidation), enzyme (trypsin), peptide tolerance: 100-500ppm, Missed Cleavages: 1 or 2.
4
Differential Protein Identification by MALDI-TOF MS
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Gels were stained with silver nitrate at room temperature for 30 min and digital images of protein dots on the gels were captured using a scanner (Seiko Epson Corporation). PDQuest 8.0 software (Bio-Rad Laboratories, Inc.) was used to identify differential spots between the Control, I/R and D-Post groups as previously described (9 (link),25 ), and these differential protein spots were excised from the gels and digested. The peptide mass fingerprint was obtained using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) with a mass spectrometer (Ultraflex III; Bruker Corporation) and compared with that from the NCBInr protein database (http://www.matrixscience.com/help/seq_db_setup_nr.html ) as reported previously (9 (link)). Peptides were extracted with 50 mM NH4HCO3:ACN (1:1, v/v). The peptide solution (3 µl) was applied to a target disk to evaporate, and mixed with 0.1 µl matrix solution (4 mg/ml in 70% ACN and 30% 0.1% TFA, v/v), spectra was obtained with MALDI TOF/TOF mass. BioTools 3.0 (Bruker Corporation) and Mascot software (Matrix Science, Inc.) were the databases used to identify proteins via peptide mass fingerprinting. NCBInr was chosen as the sequence database. The names of the differentially expressed proteins were then confirmed.
5
Peptide Synthesis and Characterization
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
EcDBS1R6 was synthesized via Fmoc chemistry using a Liberty Blue™ automated microwave peptide synthesizer (CEM Corporation), a PAL-NovaSyn TG resin (Merck Millipore), and a systematic double-coupling protocol. Fmoc-protected amino acids were purchased from Iris Biotech GMBH, and solvents from Carlo Erba. Cleavage and deprotection of the peptidyl resin were achieved by incubation of the resin with an acidic cocktail (95% TFA, 2.5% triisopropylsilane, 2.5% water) for 3 h at room temperature. After removal of the resin by filtration, the crude peptide was precipitated with cold diethyl ether (3000 × g, 15 min, 4 °C), washed with the same solvent, and dried under a stream of nitrogen. The crude peptide was subjected to purification by reversed-phase HPLC on a semi-preparative Nucleosil C-18 column (5 μm, 250 × 10 mm, Interchim SA) using a 20-60% linear gradient of acetonitrile. The homogeneity and identity of synthetic peptides were assessed by MALDI-TOF MS/MS analysis on an UltraFlex III (Bruker Daltonics). The peptide monoisotopic mass was obtained in reflector mode with external calibration, using the Peptide Calibration Standard for Mass Spectrometry calibration mixture (up to 4000 Da mass range, Bruker Daltonics).
6
Synthesis and Characterization of NDBP-5.5
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Peptide NDBP-5.5 (UniProt P0C8W1) was identified as previously described (Schwartz et al., 2007 (link)) and was synthesized by C-terminal amidation using FastBio LTDA (Ribeirão Preto, SP, Brazil). NDBP-5.5 presented >95% of purity. The molecular mass and sequence of the synthetic NDBP5.5 were confirmed by MALDI-TOF/TOF MS (UltraFlex III, BrukerDaltonics, Germany) and LIFTTM (MS/MS) as previously described (Guilhelmelli et al., 2016 (link)).
7
Polydim-I Identification via MALDI-TOF
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The fractions containing Polydim-I were subjected to identification (purity and identity) through matrix-assisted laser desorption/ionization mass spectrometry time-of flight (MALDI-TOF TOF) (UltraFlex III, Bruker Daltonics, Germany) under reflector (MS) and LIFTTM (MS/MS) positive modes. Prior to analysis, the fractions were dissolved in a saturated solution of α-cyano-4-hydroxycinnamic acid matrix in acetonitrile/water/3% trifluoroacetic acid (5/4/1). Additionally, the peptides’ mass spectra and sequencing were manually interpreted using the FlexAnalysis 3.0 software (Bruker Daltonics, Germany). The monoisotopic molecular mass of the peptide was determined as the ratio between the m/z peaks in the spread profile (m/z ratio from 600 to 3,000). Moreover, similarity searches were performed using Fasta3 programs, the Expasy12 server and BLASTP13.
8
MALDI-ToF/ToF Mass Spectrometry of Trypsin-Digested Proteins
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Proteins previously digested and desalted were prepared for MALDI-ToF/ToF mass spectrometry analysis using an Ultraflex III instrument (BrukerDaltonics, Billerica, MA). Three microliters of an α-cyan 4-hydroxicynnamic acid saturated solution (1% [w/v] α-cyano-4-hydroxycinnamic acid, 3% [vol/vol] trifluoroacetic acid, and 50% [v/v] acetonitrile) were added to 1 µL of the resuspended sample and applied onto a MALDI target plate in triplicate. Samples were dried at room temperature and the mass spectrometer was operated in reflective mode to obtain the mass spectral profile of peptide fragments generated by trypsin digestion. MS/MS spectra for selected peptides from each protein (around 60 peptides in total) were acquired in LIFT mode. Protein identification proceeded by peptide mass fingerprinting (PMF) and peptide de novo sequencing. The peptides masses obtained per protein digestion were compared to the non-redundant plant NCBI database with MASCOT software (MASCOT version 2.2, Matrix Science, London) assuming carboxyamidomethylation of cystein and methyonine oxidation as modifications. In parallel, the sequences obtained from the MS/MS spectra were compared to the non-redundant plant NCBI database and Gene Index database (http://compbio.dfci.harvard.edu/tgi/ ), using organism, max score and max identity as criteria of protein selection.
9
Proteomic Analysis of Intact Proteins
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Intact mass and in-solution trypsin digestion were analyzed using a MALDI-TOF mass spectrometer, (Bruker Daltonics Ultraflex III) in linear mode for intact proteins and reflectron mode for peptides, in the Biotechnology/Proteomics Core Facility at Kansas State University. Intact proteins were spotted with 20 mg/mL sinapinic acid in 1:1 0.1% TFA/acetonitrile. Peptide digest samples were spotted with 2,5 dihydroxybenzoic acid (50 mg/mL) in 1:1 0.1% TFA/acetonitrile. Digested mass spectra were matched against a SwissProt database for proteins within the intact mass range using mMass software (http://www.mmass.org ).
10
SALDI-TOF MS: Optimized Protocols
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
SALDI-TOF MS measurements
were performed in positive-ion and reflection modes by using an Ultra
flex III mass spectrometer (Bruker Daltonics) equipped with a 337
nm pulsed nitrogen laser. The applied acceleration voltage was +20
kV to obtain high resolution and high signal-to-noise (S/N) ratio;
each mass spectrum was generated by an average of 200 laser pulses.
We measured the same spot five times to obtain the average and standard
deviation of the intensity. The signal intensity of SALDI-TOF MS was
obtained at 30% of maximum laser power by using the CHCA organic matrix
and 40% of maximum laser power when using the TiO2 matrix
and the PDMS-coated TiO2 matrix. Data processing was performed
with the Flex analysis 3.0 software.
were performed in positive-ion and reflection modes by using an Ultra
flex III mass spectrometer (Bruker Daltonics) equipped with a 337
nm pulsed nitrogen laser. The applied acceleration voltage was +20
kV to obtain high resolution and high signal-to-noise (S/N) ratio;
each mass spectrum was generated by an average of 200 laser pulses.
We measured the same spot five times to obtain the average and standard
deviation of the intensity. The signal intensity of SALDI-TOF MS was
obtained at 30% of maximum laser power by using the CHCA organic matrix
and 40% of maximum laser power when using the TiO2 matrix
and the PDMS-coated TiO2 matrix. Data processing was performed
with the Flex analysis 3.0 software.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!