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Most cited protocols related to «Z 350»

Protein Digestion and Peptide Analysis

Cited 13 times

Samples were reduced and alkylated using dithiothreotiol (DTT; 2 mM, final concentration) and methyl methanthiosulfonate (MMTS; 5 mM final concentration). Proteins were digested overnight with endoproteinase Glu-C (from Staphylococcus aureus V8, Sigma) in 100 mM ammonium bicarbonate at 37 °C.
Peptides were separated on a reversed-phase column (Acclaim PepMap RSLC column, 2 μ, 100 Å, 75 μm × 500 mm, Thermo Fisher) by a linear gradient from 0.8 to 32% acetonitrile in 0.1% formic acid over 30 min on an RSLC nano HPLC system (Dionex). The eluting peptides were directly analyzed using a hybrid quadrupole-orbitrap mass spectrometer (QExactive, Thermo Fisher). The QExactive mass spectrometer was operated in data-dependent mode, using a full scan (m/z range 350-2,000, nominal resolution 140,000, target value 1 × 10⁶) followed by MS/MS scans of the 12 most abundant ions. MS/MS spectra were acquired at a resolution of 17,500 using normalized collision energy 30%, isolation width of 2 and the target value was set to 5 × 10⁴. Precursor ions selected for fragmentation (charge state 3 and higher) were put on a dynamic exclusion list for 10 s (dynamic exclusion tolerance is 10 ppm on QExactive by default). Additionally, the underfill ratio was set to 20% resulting in an intensity threshold of 2 × 10⁴. The peptide match feature and the exclude isotopes feature were enabled.

Dorfer V., Pichler P., Stranzl T., Stadlmann J., Taus T., Winkler S, & Mechtler K. (2014). MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra. Journal of Proteome Research, 13(8), 3679-3684.

Publication 2014

acetonitrile ammonium bicarbonate formic acid glutamyl endopeptidase High-Performance Liquid Chromatographies Hybrids Immune Tolerance Ions isolation Isotopes methyl methanethiosulfonate Peptides Proteins Radionuclide Imaging Staphylococcus aureus Tandem Mass Spectrometry Z 350

Orbitrap-based Proteome Analysis

Cited 6 times

In-solution digestion and sample preparation were performed as described previously (Wiśniewski et al., 2009 (link)). Peptides were separated using an UHPLC Dionex UltiMate® 3000 (Thermo Fisher Scientific, USA) instrument. Tryptic digests were separated by reversed-phase chromatography. Fractions were reconstituted in solvent A (water/acetonitrile, 98:2 v/v; 0.1% formic acid). The UHPLC was equipped with a Acclaim PepMap 100 trap column (100 μm × 2 cm, nanoViper C₁₈, 5 μm, 100 Å) to trap the sample, which was subsequently washed with 98% solvent A for 6 min at a flow rate of 6 μL/min, and then continuously separated on a Acclaim PepMap 100 capillary column (75 μm × 15 cm, nanoViper C18, 3 μm, 100 Å) at a flow rate of 400 nL/min. The LC analytical gradient was run at 2% to 35% solvent B over 90 min, then 35% to 95% over 10 min, followed by 90% solvent B for 5 min, and finally 5% solvent B for 15 min. Resulting peptides were electro-sprayed through a coated silica tip (PicoTip emitter, New Objective, USA) at an ion spray voltage of 2,000 eV.
The UHPLC was coupled with a heated electrospray ionization source (HESI-II) to the quadrupole-based mass spectrometer QExactive^TM Orbitrap High Resolution Mass Spectrometer (Thermo Fisher Scientific, USA). The MS spectra were acquired at a resolution of 70,000 (200 m/z) in a mass range of 350-1,800 m/z. A maximum injection time was set to 100 ms for ion accumulation. Eluted samples were used for MS/MS events, measured in a data-dependent mode for the 10 most abundant peaks (Top10 method), in the high mass accuracy Orbitrap after ion activation/dissociation with Higher Energy C-trap Dissociation (HCD) at 27 collision energy in a 100-1650 m/z mass range.

Pajarillo E.A., Kim S.H., Lee J.Y., Valeriano V.D, & Kang D.K. (2015). Quantitative Proteogenomics and the Reconstruction of the Metabolic Pathway in Lactobacillus mucosae LM1. Korean Journal for Food Science of Animal Resources, 35(5), 692-702.

Publication 2015

acetonitrile Capillaries Chromatography, Reverse-Phase Digestion formic acid Peptides Silicon Dioxide Solvents Tandem Mass Spectrometry Trypsin Z-100 Z 350

Polyacrylamide Gel Electrophoresis and Mass Spectrometry

Cited 5 times

The protein extract for each sample was diluted in Laemmli sample buffer and loaded into a 0.75 mm thick polyacrylamide gel with a 4% stacking gel casted over a 12.5% resolving gel. The run was stopped as soon as the front entered 3 mm into the resolving gel so that the whole proteome became concentrated in the stacking/resolving gel interface. Bands were stained with Coomassie Brilliant Blue and excised from the gel. Protein enzymatic cleavage (10 ug) was carried out with trypsin (Promega; 1:20, w/w) at 37 °C for 16 h as previously described^{77 (link)}. Purification and concentration of peptides was performed using C18 Zip Tip Solid Phase Extraction (Millipore). Peptides mixtures were separated by reverse phase chromatography using an Eksigent nanoLC ultra 2D pump fitted with a 75 μm ID column (Eksigent 0.075 × 250). Samples were first loaded for desalting and concentration into a 0.5 cm length 100 μm ID precolumn packed with the same chemistry as the separating column. Mobile phases were 100% water 0.1% formic acid (FA) (buffer A) and 100% Acetonitrile 0.1% FA (buffer B). Column gradient was developed in a 240 min two step gradient from 5% B to 25% B in 210 min and 25%B to 40% B in 30 min. Column was equilibrated in 95% B for 9 min and 5% B for 14 min. During all process, precolumn was in line with column and flow maintained all along the gradient at 300 nl/min. Eluting peptides from the column were analyzed using an Sciex 5600 Triple-TOF system. Information data acquisition was acquired upon a survey scan performed in a mass range from 350 m/z up to 1250 m/z in a scan time of 250 ms. Top 35 peaks were selected for fragmentation. Minimum accumulation time for MS/MS was set to 100 ms giving a total cycle time of 3.8 s. Product ions were scanned in a mass range from 230 m/z up to 1500 m/z and excluded for further fragmentation during 15 s.

Lachén-Montes M., González-Morales A., Zelaya M.V., Pérez-Valderrama E., Ausín K., Ferrer I., Fernández-Irigoyen J, & Santamaría E. (2017). Olfactory bulb neuroproteomics reveals a chronological perturbation of survival routes and a disruption of prohibitin complex during Alzheimer’s disease progression. Scientific Reports, 7, 9115.

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Publication 2017

acetonitrile brilliant blue G Buffers Chromatography, Reverse-Phase Enzymes formic acid Ions Laemmli buffer Peptides polyacrylamide gels Promega Proteins Proteolysis Proteome Solid Phase Extraction Tandem Mass Spectrometry Trypsin Z 350

Quantitative Proteomics Using SWATH-MS

Cited 5 times

For SWATH-MS, 3–5 colonies were harvested into 300 μL 6M guanidinium chloride, 50 mM Tris-HCl pH 8, 10 mM DTT and incubated at 30 °C for 30 min. Cysteines were alkylated by addition of acrylamide to 25 mM and incubation at 30 °C for 1 hour, followed by further addition of DTT to 5 mM. Proteins were precipitated by addition of 1.2 mL 1:1 methanol:acetone, incubation at −20 °C for 16 hours, and centrifugation at 18,000 rcf for 10 min. The air-dried protein pellet was resuspended in 100 μL 50 mM Tris-HCl pH 8 with 1 μg trypsin (proteomics grade, Sigma-Aldrich) and incubated at 37 °C for 16 hours. Peptides were desalted with C18 ZipTips (Millipore). Proteins were identified by information dependent acquisition LC-ESI-MS/MS analysis performed as previously described^{24 (link)} using a Prominence nanoLC system (Shimadzu) and TripleTof 5600 mass spectrometer with a Nanospray III interface (AB SCIEX). Briefly, approximately 2 μg peptides were desalted on an Aglient C18 trap and then separated on a Vydac EVEREST reversed-phase C18 HPLC column at a flow rate of 1 μL/min. Separation used a gradient of 10–60% buffer B over 45 min, with buffer A (1 % acetonitrile and 0.1 % formic acid) and buffer B (80 % acetonitrile and 0.1 % formic acid). An MS TOF scan was performed from an m/z of 350–1800 for 0.5 s followed by information dependent acquisition of MS/MS of the top 20 peptides from m/z 40–1800 for 0.05 s per spectrum, with automated CE selection. Identical LC conditions were used for SWATH-MS (Sequential Window Acquisition of all THeoretical Mass Spectra)²⁵. SWATH-MS of triplicate biological replicates was performed as previously described²⁶ with an MS-TOF scan from an m/z of 350–1800 for 0.05 s, followed by high sensitivity information-independent acquisition with 26 m/z isolation windows with 1 m/z window overlap each for 0.1 s across an m/z range of 400–1250. Collision energy was automatically assigned by Analyst software (AB SCIEX) based on m/z window ranges. Proteins were identified essentially as described^{27 (link)} using ProteinPilot (AB SCIEX), searching a database with all predicted N. meningitidis MC58 proteins and common contaminants with standard settings: Sample type, identification; Cysteine alkylation, acrylamide; ID focus, biological modifications; Enzyme, Trypsin, Search effort, thorough ID. False discovery rate analysis was performed on all searches. ProteinPilot search results were used as ion libraries for SWATH analyses. The abundance of proteins was measured automatically using PeakView (AB SCIEX) with standard settings. Comparison of protein relative abundance was performed based on protein intensities²⁶, or ion intensities using a linear mixed-effects model with the MSstats package in R^{28 (link)}. Proteins with greater than 30 % changes in abundance and with adjusted P-values < 0.05 were considered significant.

Peak I.R., Chen A., Jen F.E., Jennings C., Schulz B.L., Saunders N.J., Khan A., Seifert H.S, & Jennings M.P. (2016). Neisseria meningitidis lacking the major porins PorA and PorB are viable and modulate apoptosis and the oxidative burst of neutrophils. Journal of proteome research, 15(8), 2356-2365.

Publication 2016

Acetone acetonitrile Acrylamide Alkylation Biopharmaceuticals Buffers Centrifugation Cysteine Enzymes formic acid High-Performance Liquid Chromatographies Hydrochloride, Guanidine Hypersensitivity isolation Mass Spectrometry Methanol MS 180 Neisseria meningitidis Peptides Proteins Radionuclide Imaging Tandem Mass Spectrometry Tromethamine Trypsin Z 350

Quantitative Terpene Analysis in Plant Trichomes

Cited 5 times

Analysis of volatile terpenes was performed as described by Schilmiller et al. (2009) , with minor modifications. Four-week-old plants were used to obtain trichome exudates from either whole leaves (leaf dip method) or isolated type VI trichomes. For the former method, single leaflets were incubated at room temperature in 1 ml of methyl tertiary-butyl ether (MTBE) containing 10 ng μl⁻¹ of tetradecane internal standard. Following a 5 min incubation period with gentle shaking, the leaf was removed and its dry weight was determined. The resulting MTBE solution (2 μl) was used directly for capillary gas chromatography–mass spectrometry (GC-MS) analysis as described below. For direct analysis of type VI glands, a stretched Pasteur pipette was used to collect type VI glandular heads from the adaxial leaf surface. Collected glands, which readily stick to the glass surface, were dissolved in 100 μl of MTBE containing 10 ng μl⁻¹ tetradecane as an internal standard. A small portion (2 μl) of this extract was analysed by GC-MS on a DB-5 fused-silica column (10 m length, 0.1 mm i.d., 0.34 μm thick stationary phase; Agilent, Santa Clara, CA, USA). The GC program used an injector temperature of 280 °C. The initial column temperature was held at 40 °C for 1 min and then ramped at 40 °C min⁻¹ to 90 °C, 15 °C min⁻¹ to 110 °C, 25 °C min⁻¹ to 250 °C, and finally at 40 °C min⁻¹ to 320 °C, which was maintained for 2 min. The helium carrier gas flow was set to 0.4 ml min⁻¹. All compounds were analysed with an Agilent 6890N GC system interfaced to a 5975B quadrupole mass spectrometer (Santa Clara, CA, USA) operated using 70 eV electron ionization and mixed selected ion monitoring (m/z 85 and 93) per scan (m/z 33–350) mode. The terpene content in leaf dip samples was normalized to the dried weight of the tissue used for each extraction. The terpene content in type VI gland exudates was normalized to a specific number of isolated glands. Under the GC conditions employed, β-phellandrene co-eluted with minor amounts of limonene (data not shown). 2-Carene and α-humulene were used as standards to determine response factors for monoterpenes and sesquiterpenes, respectively.

Kang J.H., Shi F., Jones A.D., Marks M.D, & Howe G.A. (2009). Distortion of trichome morphology by the hairless mutation of tomato affects leaf surface chemistry. Journal of Experimental Botany, 61(4), 1053-1064.

Publication 2009

2-carene ARID1A protein, human Capillaries d-Limonene Electrons Ethyl Ether Exudate Gas Chromatography-Mass Spectrometry Head Helium humulene Monoterpenes Plant Leaves Plants Radionuclide Imaging Sesquiterpenes Silicon Dioxide Terpenes tetradecane Tissues Trichomes Z 350

Most recents protocols related to «Z 350»

High-Resolution Proteomics Analysis Pipeline

An EASY-nLC 1000 LC system (Thermo Fisher Scientific) interfaced via nanoSpray Flex ion source to an Orbitrap Fusion Lumos MS (Thermo Fisher Scientific) was used for MS and MS/MS analyses. A single analytical column setup using PicoFrit Emitters (New Objectives, 75 µm inner diameter) custom packed with Reprosil-Pure-AQ C18 phase (Dr. Maisch, 1.9-µm particle size, 19–21 cm column length) was applied in nLC. 2 μL of each sample was injected onto the column, followed by elution with a gradient of Solvent B from 2% to 25% at 200 nL/min for 45 min (Solvent A: 100% H₂O+ 0.1% (v/v) formic acid; Solvent B: 100% acetonitrile +0.1% (v/v) formic acid). With the nominal resolution setting of 120,000, precursors of MS1 scan (m/z 350-2,000) were obtained. Then HCD-MS2 of the five most abundant multiply charged precursors in the MS1 spectrum was acquired at the nominal resolution setting of 60,000. To trigger data-dependent fragmentation events, the minimum MS1 signal threshold was 50,000. Targeted MS/MS analysis was performed by setting up a targeted MSn (tMSn) Scan Properties panel. 30 targeted entries were included in the Mass List Table.

Chen Y.H., Tian W., Yasuda M., Ye Z., Song M., Mandel U., Kristensen C., Povolo L., Marques A.R., Čaval T., Heck A.J., Sampaio J.L., Johannes L., Tsukimura T., Desnick R., Vakhrushev S.Y., Yang Z, & Clausen H. (2023). A universal GlycoDesign for lysosomal replacement enzymes to improve circulation time and biodistribution. Frontiers in Bioengineering and Biotechnology, 11, 1128371.

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Publication 2023

acetonitrile formic acid Precipitating Factors Radionuclide Imaging Reprosil Solvents Tandem Mass Spectrometry Z 350

High-pH RPLC Fractionation and DDA MS/MS

The pooled peptide samples of each group were separated by high-pH RPLC columns (4.6 mm × 250 mm, C18, 3 μm; Waters, United States). Each pooled sample was loaded onto the column in buffer A1 (H2O, pH 10). The elution gradient was 5%–30% buffer B1 (90% ACN, pH 10; flow rate, 1 mL/min) for 30 min. The eluted peptides were collected at one fraction per minute. After lyophilization, the 30 fractions were resuspended in 0.1% formic acid and then concatenated into 10 fractions by combining fractions 1, 11, 21, and so on. To generate the spectral library, the fractions from RPLC were analyzed in DDA mode. The parameters were set as follows: the MS was recorded at 350–1,500 m/z at a resolution of 60,000 m/z; the maximum injection time was 50 ms, the auto gain control (AGC) was 1e6, and the cycle time was 3 s. MS/MS scans were performed at a resolution of 15,000 with an isolation window of 1.6 Da and a collision energy at 32% (HCD); the AGC target was 50,000, and the maximum injection time was 30 ms.

Wang Z., Liu X., Wang W., Xu J., Sun H., Wei J., Yu Y., Zhao Y., Wang X., Liao Z., Sun W., Jia L, & Zhang Y. (2023). UPLC-MS based integrated plasma proteomic and metabolomic profiling of TSC-RAML and its relationship with everolimus treatment. Frontiers in Molecular Biosciences, 10, 1000248.

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Publication 2023

Buffers cDNA Library formic acid Freeze Drying isolation Peptides Radionuclide Imaging Tandem Mass Spectrometry Z 350

Liquid Chromatography-Mass Spectrometry Protocol for Palmitoylated Protein Analysis

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Publication 2023

acetonitrile Buffers Centrifugation Dithiothreitol Enzymes formic acid Freezing Genes Iodoacetamide Liquid Chromatography Mice, House Peptides Promega Proteins Tandem Mass Spectrometry Trypsin Ultrafiltration Z-100 Z 350

Quantitative Proteomics Analysis by LC-MS/MS

Each sample was resuspended at 0.2 µg/µL with 2% acetonitrile, 0.05%. A volume of 5 µL (equivalent to 1 µg peptides) was then analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MSMS) using an U3000 RSLCnano chromatographic system (Thermo Fisher Scientific) interfaced with an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific). The chromatographic separation was done on a reverse phase Acclaim PepMap 100 C18 column (75 µm internal diameter, 3 µm particles and 500 mm length; Thermo Fisher Scientific) using a 5–45% solvent B in 90 min gradient (Solvent A: 5% acetonitrile, 0.1% formic acid; solvent B: 80% acetonitrile, 0.1% formic acid) with a flow rate of 300 nl/min while the mass spectrometer was operating in Data Dependent Acquisition mode using Thermo XCalibur software version 3.0.63. Full scan mass spectra (350 to 1800 m/z) were acquired in the orbitrap at a resolution of 120 000. Internal calibration using lock mass on the m/z 445.12003 siloxane ion was used. Each MS scan was followed by acquisition of fragmentation MSMS spectra of the most intense ions for a total cycle time of 3 s (top speed mode). The selected ions were isolated using the quadrupole analyzer in a window of 1.6 m/z and fragmented by Higher energy Collision induced Dissociation (HCD) with 35% of collision energy. The resulting fragments were detected by the linear ion trap in Rapid scan rate. Dynamic exclusion of previously fragmented peptides was set for a period of 20 s and a tolerance of 10 ppm.

Chiu C.C., Pelletier G., Stival Sena J., Roux-Dalvai F., Prunier J., Droit A, & Séguin A. (2023). Integrative analysis of green ash phloem transcripts and proteins during an emerald ash borer infestation. BMC Plant Biology, 23, 123.

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Publication 2023

acetonitrile Chromatography formic acid Immune Tolerance Liquid Chromatography Mass Spectrometry Peptides Radionuclide Imaging Siloxanes Solvents Tandem Mass Spectrometry Z 350

Measuring Bacterial Translation Elongation Rates

We measured the translation elongation rate for a subset of our strains, using the native β-galactosidase protein as a reporter as described earlier (Miller, 1972 ), with some modifications. Briefly, we induced lacZ gene expression in actively growing cultures (OD₆₀₀=0.5, n=2–3) with 0.5 mM isopropyl-β-D-thiogalactoside (IPTG). Every 15 s, we pipetted out 500 µl culture and immediately mixed it with 100 µl of chloramphenicol (3 mg/ml) to block translation. After 10 mins of incubation on ice, we added 350 µl of Z buffer (reaction buffer) and continued incubation on ice for 1 hr. Next, we added 200 µl of 12 mg/ml ONPG (o-nitro-phenyl galactopyranoside, substrate for β-galactosidase). After 1–1.5 hr of incubation at 30 °C to allow the full development of colored product (o-nitrophenol) due to enzyme activity, we stopped the reaction by adding 500 µl of 1 M Na₂CO₃. After a brief centrifugation step to collect debris (5000 g, 1 min), we transferred the supernatant to a 96-well microplate to assay the formation of o-nitrophenol by measuring OD₄₂₀. We converted OD values to Miller Units (MU) as per the original protocol, and from a plot of Miller Units (MU) of β-galactosidase vs. time, we estimated the first time point showing an increase in MU (after induction) as the time is taken to synthesize one molecule of β-galactosidase. The elongation rate (in amino acids per second) was inferred by dividing the length of the β-galactosidase protein (1019 amino acids) by this time.
The above assay informs us about the elongation rate, assuming that all other steps are equal between WT and mutant. Since, we only deleted genes encoding elongator tRNAs to create our mutant strains, this assumption likely holds. We also note that our WT strain contains an rph frameshift mutation that leads to pyrimidine starvation (Jensen, 1993 (link)) in M9 medium. Therefore, we cannot make quantitative comparisons across media. However, comparing WT and mutants growing in the same medium is appropriate.

Raval P.K., Ngan W.Y., Gallie J, & Agashe D. (2023). The layered costs and benefits of translational redundancy. eLife, 12, e81005.

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Publication 2023

2-nitrophenylgalactoside, (beta-D)-isomer Amino Acids Biological Assay Buffers Cardiac Arrest Centrifugation Chloramphenicol enzyme activity Frameshift Mutation Galactose Gene Expression Genes GLB1 protein, human Imino Acids Isopropyl Thiogalactoside LacZ Genes Nitrophenols Proteins Pyrimidines Staphylococcal Protein A Strains Transfer RNA Z 350

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Easy nlc 1200 by Thermo Fisher Scientific

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More about "Z 350"

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Whether you're working with the EASY-nLC 1000, the Q Exactive mass spectrometer, the EASY-nLC 1200, the UltiMate 3000 RSLCnano system, the Q Exactive HF-X mass spectrometer, the Q Exactive HF mass spectrometer, the Q Exactive Plus, the Q Exactive, the EASY-nLC 1200 system, or the TripleTOF 5600, this platform can help you enhance the reproducibility and accuracy of your studies.
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