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Z 300

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Reversed phase columns were prepared in-house. Briefly, a 75–360 μm inner-outer diameter bare-fused silica capillary, with a laser pulled electrospray tip, was packed with 1.7 μm diameter, 130 Å pore size, Bridged Ethylene Hybrid C18 particles (Waters) to a final length of 35 cm. The column was installed on a nanoAcquity UPLC (Waters) using a stainless steel ultra-high pressure union formatted for 360 μm outer diameter columns (IDEX) and heated to 60 °C for all runs. Mobile phase buffer A was composed of water, 0.2% formic acid, and 5% DMSO. Mobile phase B was composed of acetonitrile, 0.2% formic acid, and 5% DMSO. Samples were loaded onto the column for 12 min at 0.35 μl/min. Mobile phase B increases to 4% in the first 0.1 min then to 12% B at 32 min, 22% B at 60 min, and 30% B at 70 min, followed by a 5 min wash at 70% B and a 20 min re-equilibration at 0%B.
Eluting peptide cations were converted to gas-phase ions by electrospray ionization and analyzed on a Thermo Orbitrap Fusion (Q-OT-qIT, Thermo). Survey scans of peptide precursors from 300 to 1500 m/z were performed at 60K resolution (at 200 m/z) with a 5 × 105 ion count target. Tandem MS was performed by isolation at 0.7 Th with the quadrupole, HCD fragmentation with normalized collision energy of 30, and rapid scan MS analysis in the ion trap. The MS2 ion count target was set to 104 and the max injection time was 35 ms. Only those precursors with charge state 2–6 were sampled for MS2. The dynamic exclusion duration was set to 45 s with a 10 ppm tolerance around the selected precursor and its isotopes. Monoisotopic precursor selection was turned on. The instrument was run in top speed mode with 5 s cycles, meaning the instrument would continuously perform MS2 events until the list of nonexcluded precursors diminishes to zero or 5 s, whichever is shorter. Elite runs were performed with Survey scans of peptide precursors from 300 to 1500 m/z 60K resolution (at 200 m/z) with a 1 × 106 ion count target. Tandem MS was performed by isolation at 1.8 Th with the ion-trap, CAD fragmentation with normalized collision energy of 35, and rapid scan MS analysis in the ion trap. The data dependent top 20 precursors were selected for MS2. MS2 ion count target was set to 5 × 103 and the max injection time was 125 ms. Only those precursors with charge state +2 or higher were sampled for MS2. The dynamic exclusion duration was set to 40 s with a 10 ppm tolerance around the selected precursor and its isotopes. Monoisotopic precursor selection was turned on.
Publication 2013
acetonitrile Buffers Capillaries Cations Ethylenes formic acid Hybrids Immune Tolerance isolation Isotopes Peptides Pressure Radionuclide Imaging Silicon Dioxide Stainless Steel Sulfoxide, Dimethyl Z 300
To perform expansion microscopy, we used secondary probes (FLAP-Y) from IDT with a 5′-acrydite modification and a 3′-Atto565 label. Primary probes (CRM1 or GAPDH), were pre-hybridized with secondary probes as described in the Supplementary Protocol. smFISH experiments were performed with the Stellaris RNA FISH buffers (Biosearch Technologies) according to the provided protocol (https://www.biosearchtech.com/support/resources/stellaris-protocols), except that the final mounting step with Vectashield was omitted. Expansion was conducted as described (12 (link)) (a more detailed version is available at http://expansionmicroscopy.org/), with some modifications as explained next. Cells were grown on 18 mm coverslips to facilitate the smFISH experiments. To cast the gel, coverslips were quickly air-dried after the final washing step of the smFISH protocol. As a mold, individual wells from non-adhesive silicon insulators with an inner diameter of 4.5 mm (Grace bio-labs, Product #664206) were cut, and gently pressed on the coverslip. Gels were poured with 30 μl of the monomer solution with a cross-linker concentration of 0.2%. After 1 h, coverslips were transferred to Nunc 2-well LabTek chambers (Thermo Scientific). Proteinase K treatment was performed for 4 h at 37°C and expansion was performed as described (12 (link)). Expanded samples were embedded in 2% low melting agarose, to avoid drift during acquisition.
Three-dimensional images were acquired on a Nikon Ti Eclipse, with a LED light-source (Lumencor Spectra X light engine), a 60 × 1.4 NA objective and an Orca flash 4.0 LT sCMOS camera. Before expansion 41 z-slices with a spacing of 300 nm were acquired, after expansion 40 slices with a spacing of 600 nm. DAPI images were acquired by excitation with 390 nm at 4% for 100 ms, smFISH images at 560 nm at 40% and 500 ms.
Nuclear area was measured in 2D maximum intensity projections of DAPI images with CellProfiler (11 (link)) after automated segmentation. mRNA detection was performed with FISH-quant (5 (link)) with local-maximum detection after Laplacian of Gaussian filtering. Signal-to-noise ratio (SNR) was calculated for individual cells as the ratio of the mean amplitude of the fitted 3D Gaussian to the standard deviation of the background in a region without cells. In Supplementary Note 3, we provide carefully validated guidelines to select the best mRNA detection method in FISH-quant.
Specimen free gels were cast in 6 mm silicon tubes with varying concentrations of the cross-linker. Gels were expanded as described above for cells, but without the digestion. Diameter of expanded gels were measured, and ratio to unexpanded gels reported as expansion factor.
Publication 2016
Buffers CD3EAP protein, human Cells DAPI Digestion Endopeptidase K Fishes Fluorescent in Situ Hybridization Fungus, Filamentous GAPDH protein, human Gels Light MEV protocol Microscopy Orcinus orca RNA, Messenger Sepharose Silicon Surgical Flaps Z 300

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Publication 2014
Antibodies Argon Axon Cholinergic Receptors Cross Reactions Denervation Dental Plaque Dyes Fluorescence Forceps Helium Neon Gas Lasers IgG1 Immunoglobulins Laser Scanning Microscopy Light Mice, House Microscopy Muscle Tissue Nerve Endings Nerve Tissue Neurofilaments Neuromuscular Junction Submersion Synapses Synaptic Vesicles Synaptophysin tetramethylrhodamine Triton X-100 Z 300
An aliquot (10 µl) of an internal standard mixture containing 11 lipid classes, and 0.05 M sodium chloride (10 µl) was added to plasma samples (10 µl) and the lipids were extracted with chloroform/methanol (2∶1, 100 µl). After vortexing (2 min), standing (1 hour) and centrifugation (10000 RPM, 3 min) the lower layer was separated and a standard mixture containing 3 labeled standard lipids was added (10 µl) to the extracts. The sample order for LC/MS analysis was determined by randomization.
Lipid extracts were analysed on a Waters Q-Tof Premier mass spectrometer combined with an Acquity Ultra Performance LC™ (UPLC). The column, which was kept at 50°C, was an Acquity UPLC™ BEH C18 10×50 mm with 1.7 µm particles. The binary solvent system included A. water (1% 1 M NH4Ac, 0.1% HCOOH) and B. LC/MS grade (Rathburn) acetonitrile/isopropanol (5 2, 1% 1 M NH4Ac, 0.1% HCOOH). The gradient started from 65% A/35% B, reached 100% B in 6 min and remained there for the next 7 min. The total run time including a 5 min re-equilibration step was 18 min. The flow rate was 0.200 ml/min and the injected amount 0.75 µl. The temperature of the sample organizer was set at 10°C.
The lipid profiling was carried out on Waters Q-Tof Premier mass spectrometer using ESI+ mode. The data was collected at mass range of m/z 300–1200 with a scan duration of 0.2 sec. The source temperature was set at 120°C and nitrogen was used as desolvation gas (800 L/h) at 250°C. The voltages of the sampling cone and capillary were 39 V and 3.2 kV, respectively. Reserpine (50 µg/L) was used as the lock spray reference compound (5 µl/min; 10 sec scan frequency).
Data was processed using MZmine software version 0.60 [14] (link). Lipids were identified using internal spectral library. The normalization was performed using multiple internal standards as described in the Supporting Information Text S1. Only the identified lipid molecular species were included in further data analyses.
The Supporting Information Text S1, Figures S623 and Tables S811 also include general lipidomics platform characteristics such as internal and external standards used, calibration curves, dynamic ranges, recovery, variability, identification and quality control workflow, as well as illustrative spectra (MS and MS/MS) demonstrating how the specific species can be identified.
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Publication 2006
acetonitrile Capillaries cDNA Library Centrifugation Chloroform Isopropyl Alcohol Lipids Methanol Nitrogen Plasma Radionuclide Imaging Reserpine Retinal Cone Sodium Chloride Solvents Tandem Mass Spectrometry Z 300
Dried peptides
were dissolved in 5% formic acid and 0.1% TFA. Peptides were loaded
on a 100 μm × 150 cm column using a nano ACQUITY UHPLC
(Waters) system that was interfaced to a Q Exactive MS (Thermo Fisher
Scientific) through a nanoelectrospray ion source.39 (link) Peptides were separated by a designed gradient as indicated
(solvent A: 0.2% formic acid; solvent B: 70% ACN, 0.2% formic acid).
The peak capacity at each gradient time was calculated using formula p = 1 + tg/w, where tg is the time of the gradient
and w is the average peak width across entire LC
runs.31 (link) The peak width of individual LC
run was estimated by averaging the chromatographic peak width (4σ,
where 2σ is defined as fwhm of the corresponding extracted ion
chromatograms) of major peptide ions. Peptides in the 10 basic pH
LC subfractions were resolved similarly on this long column using
a 540 min, 15–65% buffer B linear gradient. The Q Exactive
was operated in a data-dependent mode switching between full scan
MS and up to 20 MS/MS acquisitions. The survey scans with an m/z range of 300–1600 were acquired
in the Orbitrap with 35 000 resolution at m/z = 200 and a predicted AGC value of 1 × 106 with maximal ion time of 60 ms. The ions detected in survey
scans were then sequentially isolated and fragmented by HCD at normalized
collision energy of 28 eV. The maximal ion injection time for MS/MS
was set to 60 ms at a resolution of 17 500 or 128 ms with a
resolution of 35 000. Isolation of precursor ions was performed
at 1.6 m/z window. Different dynamic
exclusion times were evaluated to maximize peptide identification
including 10, 20, 40, and 60 s. At last, 20 s was chosen for AD brain
samples. For GPF method, the operation of Q Exactive MS was similar
to the non-GPF method with minor modifications. The entire m/z range for MS1 was 300–1600 but
was divided into multiple m/z subsections,
which were described in the Results and Discussion section. Each m/z subsection had
10 m/z overlapping with adjacent
subsections.25 (link),40 (link) For data acquisition of GPF,
the cycle started at the first m/z subsection of MS1 acquisition, and its data-dependent MS/MS was
followed by the second m/z subsection
of MS1 acquisition and its data-dependent MS/MS until the full m/z range in MS1 was covered.
Publication 2014
AT 17 Buffers Chromatography formic acid Ions isolation Peptides Radionuclide Imaging Solvents Tandem Mass Spectrometry Z 300

Most recents protocols related to «Z 300»

P. aeruginosa ID40 parental and mutant strains were grown overnight in LB medium. The OD600 of overnight cultures (LB medium) was measured. 100 ml LB bacteria cultures with an initial OD600 of 0.05 per ml were grown for 6 h. Cells were harvested and OD600 measured. Bacteria were pelleted and resuspended in 20 ml 50 mM Tris-HCL buffer, pH 7.6 to a final concentration of OD600 = 5/ml (final OD600 = 100). Subsequently, bacteria were centrifuged at 3,000 g for 10 min. The supernatant was discarded and the pellet frozen at –80 °C. The next day, bacteria were resuspended in 400 µl water and the cultures boiled for 15 min at 95 °C. Cultures were cooled down to and centrifuged at room temperature at 16,000 g for 10 min. 200 µl of the supernatant were added to 800 µl ice-cold acetone (MS grade, Sigma 34850-2.5 L) to precipitate remaining proteins in the samples. Samples were then centrifuged at 4 °C at 16,000 × g for 10 min. The supernatant was transferred in a new tube and the cytosolic fraction was dried under vacuum for 2 h at 55 °C in a Speedvac (Eppendorf). Pellets were then stored at 4 °C. The dry cytosolic fractions were then dissolved in 50 µl Millipore water. 5 µl of the samples were subjected to LC-MS analysis with an UltiMate 3000 LC system (Dionex) coupled to an electrospray ionization-time of flight mass spectrometer (MicrO-TOF II; Bruker) that was operated in positive-ion mode in a mass range 180 m/z to 1,300 m/z. Metabolite separation was achieved with a Gemini C18 column (150 by 4.6 mm, 110 Å, 5 μm; Phenomenex) at 37 °C with a flow rate of 0.2 ml/min in accordance with a previously described 45 min gradient program40 (link) with small modifications: 5 min of washing with 100% buffer A (0.1% formic acid, 0.05% ammonium formate in water), followed by a linear gradient over 30 min to 40% buffer B (acetonitrile) and a 10 min column re-equilibration step with 100% buffer A. Peptidoglycan (PG) metabolites were shown in Data Analysis (Bruker) by extracted ion chromatograms (EICs) and the area under the curves of the respective EICs were calculated in Prism 8 (GraphPad). The theoretical m/z values of the PG metabolites investigated are 276.108 m/z for anhMurNAc, 479.187 m/z for GlcNAc-anhMurNAc, 648.272 m/z for anhMurNAc-3P, 851.352 m/z for GlcNAc-anhMurNAc-3P, 790.347 m/z for anhMurNAc-5P, 680.110 m/z for UDP-MurNAc, and 1194.349 (597.678 2+) for UDP-MurNAc 5 P.
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Publication 2023
21-hydroxy-9beta,10alpha-pregna-5,7-diene-3-ol-20-one Acetone acetonitrile anhydro-N-acetylmuramic acid Bacteria Buffers Cells Cold Temperature Cytosol formic acid formic acid, ammonium salt Freezing Parent Pellets, Drug Peptidoglycan prisma Proteins Pseudomonas aeruginosa Strains Tromethamine Vacuum Z 300
Phosphopeptides were separated by liquid chromatography on the EASY-nLC 1200 system (Thermo Fisher Scientific) for 120 minutes. Briefly, phosphopeptides were loaded onto a reverse phase trap column (Thermo Scientific Acclaim PepMap100; 100 μm × 2 cm, nanoViper C18) connected to a C18-reversed phase analytical column (Thermo Scientific Easy Column; 10-cm long, 75-μm inner diameter, 3 μm resin). The phosphopeptides were separated by reversed-phase chromatography using a binary buffer system consisting of 0.1% formic acid (buffer A) and 80% acetonitrile in 0.1% formic acid (buffer B) at a flow rate of 300 nl/minute. MS data were analyzed on a Q-Exactive HF mass spectrometer (Thermo Fisher Scientific) using a data-dependent top 10 method, with a maximum injection time of 10 ms, scan range of 300–1800 m/z and automatic gain control target of 3e6. Survey scans were acquired at a resolution of 70 000, and the resolution for HCD spectra was set to 17 500. Normalized collision energy was 30 eV, and the underfill ratio was set to 0.1%.
MS data were processed with Proteome Discoverer version 2.4. Enzyme specificity was set to that of trypsin, allowing for cleavage up to two missed cleavage sites. Carbamidomethyl (C), TMT 6/10 plex (N-term) and TMT 6/10/16 plex (K) were selected as fixed modifications, while Oxidation (M), TMT 6/10/16 plex (Y) and phospho (S/T/Y) was added as variable modifications. The FDR for phosphopeptides was set to 0.01. Searches were performed against the Gallus gallus UniProt FASTA database (February 2020) containing 34 878 entries. Quantification of phosphopeptides was normalized by subtracting the median intensity of each sample. Phosphopeptides that changed by > 1.5 fold with a Student t-test p < 0.05 were considered significantly regulated.
With regard to the kinase–substrate enrichment analysis, iGPS [58 (link)] was used to identify any phosphosite on a kinase. GSEA version 4.1.0 [59 (link)] was used to identify significantly enriched kinases using a ranked fold change of all quantified phosphopeptides. The corresponding p value and normalized enrichment score were assigned for each kinase.
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Publication 2023
acetonitrile Buffers Chickens Chromatography, Reverse-Phase Cytokinesis Enzymes formic acid Liquid Chromatography Phosphopeptides Phosphotransferases Proteome Radionuclide Imaging Resins, Plant Student Trypsin Z 300
The mass spectrometry proteomic data have been deposited to the ProteomeXchange Consortium via the PRIDE [87 (link)] partner repository with the dataset identifier PXD034057.
From each sample, total proteins were proteolyzed with LysC (Wako Chemicals, Neuss, Germany) and trypsin (Promega) using a suspension trapping protocol (S-Trap, Protifi) to remove SDS according to the manufacturer’s instructions. Briefly, samples were reduced and carbamidomethylated, followed by acidification with phosphoric acid and addition of methanol to a final concentration of >70% before loading to the trap columns. Proteins were washed while trapped on column, then digested on column with LysC (2 hours at RT) followed by trypsin (overnight, at 37 C). Peptides were collected by centrifugation and acidified. Eluted peptides were analyzed on a Q Exactive HF mass spectrometer (Thermo Fisher Scientific) in the data dependent mode. Approximately 0.5 μ g peptides per sample were automatically loaded to the online coupled ultra-high-performance liquid chromatography (UHPLC) system (Ultimate 3000, Thermo Fisher Scientific). A nano trap column was used (300- μ m ID X 5mm, packed with Acclaim PepMap100 C18, 5 μ m, 100 Å; LC Packings) before separation by reversed phase chromatography (Acquity UHPLC M-Class HSS T3 Column 75 μ m ID X 250 mm, 1.8 μ m; Waters) at 40 C. Peptides were eluted from the column at 250 nL/min using increasing ACN concentrations (in 0.1% formic acid) from 3% to 41% over a linear 95-min gradient. MS spectra were recorded at a resolution of 60 000 with an AGC target of 3 × 106 and a maximum injection time of 50 ms from 300 to 1’500 m/z. From the MS scan, the 10 most abundant peptide ions were selected for fragmentation via HCD with a normalized collision energy of 28, an isolation window of 1.6 m/z, and a dynamic exclusion of 30 s. MS/MS spectra were recorded at a resolution of 15’000 with an AGC target of 105 and a maximum injection time of 50 ms. Unassigned charges and charges of +1 and above +8 were excluded from precursor selection.
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Publication 2023
Centrifugation Chromatography, Reverse-Phase formic acid High-Performance Liquid Chromatographies Ions isolation Mass Spectrometry Methanol Peptides Phosphoric Acids Promega Proteins Radionuclide Imaging Tandem Mass Spectrometry TRAP protocol Trypsin Z 300
Digested samples were analysed by LC-MS/MS using an UltiMate® 3000 Rapid Separation LC (RSLC, Dionex Corporation, Sunnyvale, CA) coupled to a Q Exactive HF (Thermo Fisher Scientific, Waltham, MA) mass spectrometer. Mobile phase A was 0.1% formic acid in water and mobile phase B was 0.1% formic acid in acetonitrile and the analytical column was a 75 mm x 250 μm, i.d. 1.7 μM, CSH C18 column (Waters, UK). 1 µl of the sample was transferred to a 5 µl loop and loaded onto the column at a flow of 300 nl/min for 5 minutes at 5% B. The loop was then taken out of line and the flow was reduced from 300 nl/min to 200 nl/min in 0.5 minutes. Peptides were separated using a gradient from 5% to 18% B in 63.5 minutes, then from 18% to 27% B in 8 minutes and finally from 27% B to 60% B in 1 minute. The column was washed at 60% B for 3 minutes before re-equilibration to 5% B in 1 minute. At 85 minutes, the flow was increased to 300 nl/min until the end of the run at 90 minutes. Mass spectrometry data was acquired in a data dependent manner for 90 minutes in positive ionization mode. Peptides were selected for fragmentation automatically by data dependant acquisition on the basis of the top 12 peptide ions with m/z between 300 to 1750 Th and a charge state of 2, 3 or 4 with dynamic exclusion set at 15 sec. MS1 resolution was set at 120,000 with an AGC target of 3e6 and a maximum fill time set at 20 ms. MS2 resolution was set to 30,000, with an AGC target of 2e5, a maximum fill time of 45 ms, isolation window of 1.3 Th and a collision energy of 28 eV.
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Publication 2023
acetonitrile formic acid Ions isolation Peptides Tandem Mass Spectrometry Z 300
The analytical column was directly connected to a 10 μm ZDV emitter (Bruker) inside of the Bruker captive source. The capillary voltage was set to 1700 V with the dry gas set at 3.0 L/min and 200° C. Data was acquired by diaPASEF on a Bruker timsTOF SCP with the ion accumulation and trapped ion mobility ramp set to 166 ms. DIA scans were optimized and acquired with 90 m/z windows spanning 300 to 1200 m/z and 0.6 to 1.43 1/K0. A 0.86 s cycle time included one full MS1 scan followed by 4 trapped ion mobility ramps to fragment all ions within the defined region.
Publication Preprint 2023
Capillaries Ions Radionuclide Imaging Range of Motion, Articular Z 300

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More about "Z 300"

The Z 300 is a powerful artificial intelligence-driven comparison and optimization tool developed by PubCompare.ai, a cutting-edge platform that helps researchers enhance the reproducibility and accuracy of their work.
Leveraging advanced AI algorithms, the Z 300 tools facilitate data-driven discovery, allowing users to identify the best protocols and products for their specific research needs.
This innovative platform enables researchers to locate and analyze protocols from literature, preprints, and patents, ensuring they have access to the latest and most relevant information.
The Z 300 comparison and optimization tools can be particularly useful when working with mass spectrometry-based techniques, such as those utilizing the Q Exactive, Q Exactive HF, LTQ-Orbitrap Velos, or LTQ Orbitrap XL mass spectrometers, as well as the EASY-nLC 1000 liquid chromatography system and Xcalibur software.
By harnessing the power of AI, the Z 300 tools can help researchers make more informed decisions and drive their work forward, ensuring they are using the most effective protocols and products for their specific research needs.
With the Z 300, researchers can experience the future of data-driven discovery and enhance the reproducibility and accuracy of their findings.