Proteins were eluted in 50% acetonitrile containing α-cyano-4-hydroxycinnamic acid directly applied onto the target metal plate and analyzed by MALDI-TOF MS on a Bruker Ultraflex (Bruker Daltonics, Bremen, Germany). Peptide mass spectra were analyzed using embedded flexAnalysis software. Calibration of peptide spectra was internally performed using trypsin autolytic proteins (842.51, 1,045.56, and 2,211.10 Da). Protein identity search was performed using the Mascot protein identification server viahttp://www.matrixscience.com/ using the model plant “Arabidopsis” protein database. The set parameters included one miscut, alkylation, and partial oxidation of methionine. Others were Arabidopsis thaliana such as taxonomy, pI, and Mr determined from gel migration spot position with mass tolerance of 0.1 Da. The statistical significance of all identified proteins was evaluated according to Z-value and sequence coverage based on Mascot algorithms. Subsequent gene ontology and enrichment analysis were performed using Gene Ontology Resource (http://geneontology.org/ ) and UniProt database via (https://www.uniprot.org/ ).
Ultraflex
Manufactured by Bruker
Sourced in Germany, United States
The Ultraflex is a high-performance mass spectrometry system designed for a wide range of analytical applications. It features advanced technology for efficient and accurate measurements.
Automatically generated - may contain errors
Lab products found in correlation
Axima qit, by Shimadzu (3 mentions)
C18 ziptip, by Merck Group (2 mentions)
Mascot software, by Matrix Science (2 mentions)
Biotools, by Bruker (2 mentions)
Tg dta7300, by Seiko Instruments (2 mentions)
Mtp 384 ground steel target plate, by Bruker (2 mentions)
Flexanalysis 2, by Bruker (2 mentions)
Mtp anchor chip 400 384 tf, by Bruker (1 mentions)
α cyano 4 hydroxycinnamic acid, by Nacalai Tesque (1 mentions)
Dataanalysis v4, by Bruker (1 mentions)
Jnm la 300, by JEOL (1 mentions)
V 650 spectrophotometer, by Jasco (1 mentions)
Oxygraph plus system, by Hansatech (1 mentions)
Silica gel 60n, by Kanto Chemical (1 mentions)
Jnm a400, by JEOL (1 mentions)
Imageprep, by Bruker (1 mentions)
Lift technology, by Bruker (1 mentions)
α cyano 4 hydroxycinnamic acid, by Fujifilm (1 mentions)
Zeba spin desalting column, by Thermo Fisher Scientific (1 mentions)
Aktaexplorer 10 s system, by GE Healthcare (1 mentions)
47 protocols using ultraflex
1
MALDI-TOF-MS Protein Identification Workflow
2
Genotyping of ERBB4 Variants
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Two ERBB4 germline single nucleotide variants, −782G>T and −815A>T [11] (link), and nine previously described somatic ERBB4 mutations [15] (link) were genotyped to establish allele and genotype frequencies in the FinHer cohort. Genotyping was carried out with matrix-assisted laser desorption ionization/time of flight mass spectrometry using SpectroCHIP microarray and Bruker Autoflex (Sequenom) as well as MTP Anchor Chip 400/384 TF and Bruker Ultraflex (Bruker Daltonics) [11] (link). The ERBB4 variant analyses were conducted using tumor DNA, as no DNA from non-neoplastic tissue was available. However, when the variants were initially identified from tumor DNA of colorectal cancer patients, the variants were confirmed to be germ-line in all cases [11] (link).
3
MALDI-TOF and MALDI-QIT-TOF Mass Spectrometry of Glycans
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MS spectra were acquired using a matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometer (Ultraflex; Bruker Daltonik, Bremen, Germany). Ions were generated using a 337-nm nitrogen laser and were accelerated to 20 kV for reflectron mode and to 25 kV for linear mode. All spectra were obtained using a positive ion mode with delayed extraction. For MS/MS spectra acquisition, a MALDI-quadrupole ion trap (QIT)-TOF mass spectrometer (AXIMA-QIT; Shimadzu Corp., Kyoto, Japan) was used. Argon gas was used as a collision gas for collision-induced dissociation. For sample preparation, 0.5 μL of 2,5-dihydroxybenzoic acid (2,5-DHB; 10 mg/mL) in 30% ethanol was spotted onto a target plate (MTP 384 target plate ground steel [Bruker Daltonik] for Ultraflex and 384 specular surface stainless steel plate [Shimadzu Corp.] for AXIMA-QIT) and dried. For sialoglycans, at 95:5 mixture of 2,5-DHB and 2,5-DHB-Na was used as a matrix. Subsequently, an aliquot (0.5 μL) of the glycan solution was spotted onto the matrix crystal and dried.
4
Identification of Scythe-interacting Proteins in Xenopus Embryos
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Synthetic mRNA encoding C-terminally S-epitope (KETAAAKFERQHMDS)-tagged Xenopus BAG6 (Scythe) was microinjected into the 2-cell stage Xenopus embryos. Eighteen hours after injection, developing embryos were lysed with immunoprecipitation buffer (20 mm Tris-HCl, pH 7.5, 150 mm NaCl, 1 mm EDTA, 1% Nonidet P-40, 5 μg/ml leupeptin, 1 μg/ml pepstatin, 2 μg/ml aprotinin, 1 mm dithiothreitol), and Scythe-interacting proteins were affinity-purified using S-protein-agarose beads. Precipitates were subjected to SDS-PAGE and PMF analysis. PMF was performed basically as described by Minami et al. (10 (link)). Trypsin-digested peptides were desalted using a ZipTip-C18μ (Millipore) and mixed with 5 mg/ml α-cyano-4-hydroxycinnamic acid (Nacalai Tesque) in 0.1% trifluoroacetic acid and 50% (v/v) acetonitrile. The PMFs of proteins were obtained by MALDI-TOF/TOF MS on Ultraflex (Bruker Daltonics). A database search was performed using Mascot.
5
MALDI-TOF MS Analysis of Peptides
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The peptide digested in solution was mixed with fourfold saturated solution of sinapic acid (SA) in a mixture of trifluoroacetic acid (TFA) and acetonitrile [0.1% TFA and acetonitrile (2:1, v/v)]. Tenfold amount of 0.1% TFA was added, ultrasonic treatment (5 min) and centrifugation (20,400 g, 5 min) were performed, the supernatant was discarded and the sample was cleaned. Saturated solution of SA in ethanol was dropped onto a MALDI target plate and allowed to dry to form a thin layer. The cleaned sample was resolved with 0.1% TFA and dropped onto the thin layer, allowed to dry, and subjected to MALDI-TOF MS (Ultraflex, Bruker Daltonics, Billerica, MA). The mass spectra were acquired in positive linear mode range of m/z 3000–30,000. Theoretical molecular weight was calculated with Sequence Editor software (Bruker Daltonics).
6
MALDI-TOF Mass Spectrometry of PNWP-L
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A small amount (1 mg) of the PNWP-L was mixed with 10 μL of 2,5-dihydroxybenzoic acid (DHB) matrix (50 mg/mL of DHB in 50% methanol and 0.1% TFA). The spectrum was recorded in an Ultraflex (Bruker Daltonics, Bremen, Germany) using negative and positive ion modes. Raw data were processed using DataAnalysis V4.1 (Bruker Daltonics).
7
Synthesis and Characterization of Si-Containing Polymers
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The molecular weights and PDI values were determined by gel permeation chromatography on a Shimadzu HPLC-8020 using a calibration curve based on polystyrene standards in CHCl3 at 40°C. 1H-NMR spectra were recorded on JEOL JNM-LA 300 or 400 MHz instruments using CDCl3 or DMSO-d6 as the solvent. MALDI-TOF-MS spectra were recorded on a Bruker Daltonics Ultraflex using dithranol as the matrix (10 mg ml−1 in CHCl3). UV–vis spectra were recorded on a JASCO V-650 spectrophotometer. XRD was performed by Rigaku Smart Lab. The incident angle for the in-plane measurements was 0.2°. 2D GIWAXS was measured on the BL19B2 and BL46XU beamlines at SPring-8 with an incident angle of 0.12°. The film samples were prepared by spin coating the polymer solution in CHCl3 on the Si/SiO2 (300 nm) substrate at 2500 r.p.m. for 60 s. The concentrations were 7 mg ml−1, 9 mg ml−1, 11 mg ml−1, 12 mg ml−1 and 15 mg ml−1 for Si0, Si30, Si50, Si70 and Si100, respectively. Photoelectron spectroscopy in air was performed on a Riken Keiki AC-2 instrument. The solubility of the polymers was tested by weighing out approximately 10 mg of the samples into a vial and adding CHCl3 by 50 µl incrementally until the complete dissolution of the polymer was observed by the naked eye.
8
Oxygen Consumption Assay for FIH Activity
9
Immunoconjugate Characterization by MALDI-ToF
10
MALDI-TOF Analysis of Permethylated Glycans
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The MS spectra of the permethylated glycans were acquired in reflectron positive ion mode using a matrix-assisted laser desorption ionization (MALDI)-time-of-flight (TOF) mass spectrometer (UltraFlex; Bruker-Daltonics) equipped with a 337 nm pulsed nitrogen gas laser. 2,5-Dihydroxybenzoic acid (2,5-DHB) was used as the matrix. For sample preparation, 0.5 µl of 2,5-DHB solution (10 mg/ml in 30% ethanol) was deposited onto a MALDI target plate and dried. Then 0.5 µl of the sample solution was deposited over the dried spot of 2,5-DHB and dried. Tandem mass spectrometry was performed using a MALDI-quadrupole ion trap (QIT)-TOF mass spectrometer (AXIMA-QIT; Shimadzu Corp.) in a positive ion mode. Argon gas was used as the collision gas for collision-induced dissociation.
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