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Human recombinant proMMPs and in vitro activated MMPs were obtained from Invitek [ 44] and were labeled with the [I]-Bolton-Hunter reagent according to the manufacturer's instructions (PerkinElmer, Rodgau, Germany) before the buffer was exchanged for phosphate-buffered saline (PBS) with 0.05% (vol/vol) Tween 20 by gel filtration as described previously [ 45].
Slow-exchanging amide protons identified in the 2D 15N-1HSQCQC spectra recorded after the H2O buffer was exchanged for a D2O buffer were used in the structure calculated with the NOE distance restraints to generate hydrogen bonds for the final structure calculation as previously described in the literature (Chakravarty et al., 2009).
The reaction buffer was exchanged for PBS using Amicon Ultra (Merck-Millipore, Darmstadt, Germany).
Prior to CE-MS analysis, the formulation buffer was exchanged for water using a MWCO filter of 3 kDa.
Storage buffer was exchanged for crystallization buffer [0.1 mM MgCl2, 0.2 mM ThDP, and 25 mM NaHEPES (pH 7.0)].
Then, the cathode buffer was exchanged for cathode buffer B/10 (buffer B but containing only 0.002% Coomassie Blue G250) and gels were run at 100 V [anode buffer: 50 mM Bis-Tris (pH 7)].
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Buffer was exchanged every 30 min for 4 h and degradation was monitored via absorption at 280 nm to assess the production of tryptophan-containing degradation fragments using an Infinite M200 Pro microplate reader.
The sample buffer was exchanged to 50 mM NH4HCO3 for trypsin digestion and to 100 mM Tris-HCl, 10 mM CaCl2, pH 7.6 for endoproteinase Arg-C digestion, using Amicon Ultra Centrifugal Filter Devices (Millipore Corporation Billerica, MA).
The buffer was exchanged to 100 mM AmAc for MS analysis.
To compensate for evaporation, the buffer was exchanged at regular intervals of 1 h.
For MS, the buffer was exchanged to 100 mM AmAc, pH 7.5, using micro Bio-Spin columns (Bio-Rad LAmiconories) or Amicon 10 kDa MWCO (Millipore).
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