Fungi were identified using Matrix Assisted Laser Desorption/ionization Time-Of-Flight (MALDI-TOF) mass spectrometry (BrukerDaltonics, Germany). A standard method was used for protein extraction, according to the manufacturer’s recommendations27 (link),29 (link). One μl of each protein extraction supernatant and the matrix HCCA (a-cyano-4-hydroxycinnamic acid) were spotted on the MSP96 target (Bruker Daltonics, Germany) with a positive control (Candida albicans) and a negative control (the matrix). The data acquisition was performed on the MALDI Biotyper (Microflex LT system; Bruker Daltonics GmbH, Bremen, Germany) using Flex ControlTM software and MALDI BioTyper RTC identification software (Bruker Daltonics).
Flexcontrol software
Manufactured by Bruker
Sourced in Germany, United States
FlexControl is a software platform designed to control Bruker's analytical instruments, including NMR and mass spectrometry systems. The software provides a unified interface for instrument operation, data acquisition, and basic data processing functions.
Automatically generated - may contain errors
Lab products found in correlation
Flexanalysis software, by Bruker (18 mentions)
Microflex lt maldi tof mass spectrometer, by Bruker (5 mentions)
Microflex lt mass spectrometer, by Bruker (5 mentions)
Maldi biotyper v 3, by Bruker (5 mentions)
Flexanalysis, by Bruker (4 mentions)
Ultraflextreme mass spectrometer, by Bruker (4 mentions)
Peptide calibration standard, by Bruker (4 mentions)
Microflex, by Bruker (4 mentions)
Flexanalysis v 3, by Bruker (4 mentions)
Microflex lrf maldi tof mass spectrometer, by Bruker (3 mentions)
Ultraflex 2 maldi tof tof instrument, by Bruker (3 mentions)
Flexanalysis 3, by Bruker (3 mentions)
Maldi biotyper 3, by Bruker (3 mentions)
Ultrafextreme maldi tof tof instrument, by Bruker (2 mentions)
Clinprotools v3, by Bruker (2 mentions)
Autoxecute flex control software, by Bruker (2 mentions)
Maldi biotyper compass explorer v4, by Bruker (2 mentions)
Microflex maldi tof mass spectrometer, by Bruker (2 mentions)
Biotyper 3, by Bruker (2 mentions)
Maldi biotyper software, by Bruker (2 mentions)
97 protocols using flexcontrol software
1
MALDI-TOF Mass Spectrometry for Fungal Identification
2
MALDI-TOF MS Protocol for Fungal Identification
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All isolates were identified by MALDI-TOF MS using the Mass Spectrometry Identification 2 (MSI 2) platform database [16 ]. Fungal proteins were extracted from a mature subculture on Malt extract-agar medium (VWR, Rosny-Sous-Bois, France) using a previously described extraction protocol with minor modifications [17 (link)]. Briefly, a loop-full of mycelial colonies was transferred into a 1.5 mL microtube containing 300 μL of pure water and 900 μL of pure ethanol. After two centrifugations at 13,000× g for 2 min, the pellet was suspended in 25 μL of 70% formic acid and 25 μL of 100% acetonitrile. A sample of 1.0 μL of the fungal extract supernatant was spotted on a 96-spot polished steel plate in duplicate (Bruker Daltonics, Billerica, MA, USA) and allowed to completely dry at room temperature. Then, 1 μL of the IVD matrix HCCA portioned solution (Bruker Daltonik, Ref: 8290200, Billerica, MA, USA) was added. Protein spectra were analyzed using FlexControlTM software with and the MBT compass software (Bruker, Billerica, MA, USA) and compared with Mass Spectrometry Identification (MSI) platform database 2. Identification was retained when the MSI score was above or equal to 20%. If several identification results were proposed for the same specimen, only the result with the best score was retained.
3
Characterization of Isolate CH-KOV3 by MALDI-TOF MS
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Isolate CH-KOV3 was characterized using a Bruker Autoflex II MALDI-TOF MS (Bremen, Germany) equipped with a UV nitrogen laser (337 nm) and a dual microchannel microplate detector. Together with whole (intact) bacteria, crude cell extracts were prepared accordingly [30] and also analyzed as previously described [31] . Spectra were recorded by Flex Control software (Bruker Daltonics, Bremen, Germany), and samples were analyzed in six replicates using Flex Analysis (Bruker Daltonics, Bremen, Germany). For each measurement, at least 3,000 individual spectra (300 shots at laser power from 10 different points of a dried sample spot) were collected and averaged to obtain MALDI-TOF MS spectrum. External calibration was performed with protein standards (Bruker Protein Test Standard, Bruker Daltonics, Bremen, Germany). MALDI BioTyper db 6903 software was used for the protein profile analysis by pattern matching with the libraries.
4
MALDI-TOF Analysis of His6-Pga Proteins
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His6-Pga59 and His6-Pga59V32,33N integrity and purity were analysed on a Bruker UltrafeXtreme MALDI-TOF/TOF instrument. A volume of 15 μL of protein was passed through a ZipTip C4 and eluted on an MTP 384 ground steel target plate (Bruker-Daltonics, Germany) with 2 μL of 20 mg mL−1 α-Cyano-4-hydroxycinnamic acid in 50% acetonitrile, 0.1% trifluoroacetic acid as matrix solution. Data were acquired using Flexcontrol software (Bruker-Daltonics, Germany) and shots were recorded in positive ion linear mode. Mass spectra were externally calibrated in the m/z range of 5–20 kDa with Protein I (Bruker-Daltonics, Germany) and analysed with the Flexanalysis software (Bruker).
5
MALDI-TOF/TOF Imaging of Spinal Cord Tissue
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Samples on ITO-coated glass slides were sprayed with 1 mL matrix solution (40 mg/mL 2,5-dihydroxybenzoic acid), 20 mM potassium acetate, 70% methanol) (Bruker Daltonics) using a 0.2 mm nozzle caliber airbrush (Procon Boy FWA Platinum; Mr. Hobby, Tokyo, Japan). Distance between the nozzle tip and the slice surface was kept at 10 cm, and spraying was performed for 15 min for uniform matrix deposition. Positive ions of the spinal cord were detected using a MALDI-TOF/TOF-type instrument (ultraflex II TOF/TOF;Bruker Daltonics) equipped with a 355 nm Nd:YAG laser. The laser was set to the minimum spot size with 20% laser power. Mass spectra ranging from mass-to-charge ratio (m/z) 500 to 1000were collected. Laser scan pitch was set to 50 μm. The calibration of m/z values was performed for each IMS measurement using calibration standard substances: 2,5-dihydroxybenzoic acid, bradykinin (Sigma-Aldrich, St Louis, MO, USA), and angiotensin II (Sigma-Aldrich). Regions of interest (ROIs) in spinal cord were determined by comparison with the HE staining result from consecutive tissue sections. Signals were collected using flexControl software (Bruker Daltonics) and reconstruction of ion images (normalized by total ion current) was performed with flexImaging4.0 software (Bruker Daltonics).
6
Characterization of Captured miRNAs via MALDI-TOF-MS
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Captured miRNAs were purified with a Zip Tip C18 column (Millipore, Billerica, MA, USA) according to the manufacturer’s protocol. Purified samples were mixed with an aqueous solution of 3-hydroxypicolinic acid (Bruker Daltonics, Bremen, Germany) at a ratio of 1:1 (v/v) and applied to the target plate. One microliter of the mixture was applied to an MTP AnchorChip 384 target plate (Bruker Daltonics) and air-dried at room temperature. MALDI-TOF-MS analysis was performed with an ultrafleXtreme MALDI-TOF/TOF mass spectrometer (Bruker Daltonics) operated in negative ion and reflectron modes. Spectra were manually acquired using FlexControl software (v.3.3.108.0) (Bruker Daltonics). An analysis of the RNAs following hydrazine treatment revealed that the peaks contained m5C25 (link). Methylated adenines were determined to be 6 mA by sequential MS analysis following treatment with dimethylsulfate, which preferentially alkylates the N1 of adenines in RNA26 (link).
7
Identification of Acinetobacter baumannii Strains
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Clinical isolates of Acinetobacter baumannii G7 and T-10 were used in this study. A. baumannii strains G7 –isolated in Georgia from an injured soldier during the Georgian–Russian War in 2008 as previously described (Kusradze et al., 2011 (link)), was used for isolation and concentration of the reported phage. Strain T-10 was isolated from a patient in the hospital de la Timone, Marseille, France. Bacteria were grown at 37°C in Brain Heart Infusion broth and agar, and in Herellea Agar (Jawad et al., 1994 (link)). Matrix-assisted Laser Desorption Time-of-Flight Mass Spectrometry (MALDI-TOF MS) (Autoflex, Bruker Daltonics) with the flex control software (Bruker Daltonics) was used for identification these strains. A score value >1.9 is considered adequate for identification at the species level (Seng et al., 2009 (link)).
8
MALDI-TOF Mosquito Leg Profiling
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The spectral profiles obtained from the mosquito legs were visualised using a Microflex LT MALDI-TOF mass spectrometer with FlexControl software (version 3.3; Bruker Daltonics). The spectra were acquired in a positive linear mode at a laser frequency of 50 Hz. The accelerating voltage was 20 kV, and the extraction delay time was 200 ns. Each spectrum corresponded to the ions obtained from the 240 laser shots performed in six regions at the same location and acquired automatically using the AutoXecute Flex Control software (version 2.4; Bruker Daltonics). The MS profiles were visualised using the FlexAnalysis v3.4 software, MALDI Biotyper Compass Explorer v4.1.70 (Bruker Daltonics), and ClinProTools v3.0 software (Bruker Daltonics) was used for data processing.
9
MALDI-TOF Analysis of USP14 Compound Binding
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Recombinant USP14 protein was desalted to remove interfering reducing agent on 30 kDa cut-off spin columns (Merck) and resuspended in water. For MALDI-TOF analysis of compound binding, 10 µg USP14 protein was incubated with 10 µM of selected compounds for 45 minutes at room temperature. Samples were then desalted to remove unbound compound on 30 kDa cut-off spin columns and resuspended in water. Approximately 0.25 µg sample was loaded onto polished stainless steel MALDI-TOF plates with sinapic acid (3,5-dimethoxy-4-hydroxycinnamic acid, Sigma) as matrix substance and air-dried until completely dry. Whole protein mass spectra were acquired on an UltrafleXtreme MALDI-TOF mass spectrometer (Bruker Daltonics) instrument operated in the linear positive ion mode with flexControl software (Version 3.4, Bruker Daltonics). Each spectrum was the accumulation of approx. 5000 laser shots for the sample spots. The MS spectra were externally calibrated using the Protein Calibration Standard II mixture (Bruker Daltonics). The MS spectra obtained were analyzed using flexAnalysis software (Version 3.4, Bruker Daltonik).
10
MALDI-TOF Mass Spectrometry of Desalted Peptides
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The desalted peptides were mixed with a 1:1 (v/v) mixture of α-cyano-4-hydroxy cinnamic acid (HCCA) saturated with a solution comprising 30% methyl cyanide and 0.1% methanoic acid, applied to a polished steel plate, and subjected to mass characterization by a Microflex® MALDI-TOF mass spectrometer (Bruker Daltonics, Bremen, Germany), which was operated in positive ion mode and reflector detector, and previously calibrated with an external standard (700–1800 Da). The data were processed by means of the FlexControl Software (Version 3.0, Bruker Daltonics GmbH).
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