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Two scan events were applied: ion trap (ITMS) for quantification, including selected reaction monitoring (SRM) on XMP (m/z 347/153 between 0 and 4 min) and c-di-GMP (m/z 691/540 between 4 and 6.5 min) and orbitrap fullscan (FTMS) for accurate mass identification, using a resolution of 30000.
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Excised spots were subjected to mass-fingerprint identification using Maldi-TOF MS analysis as described elsewhere [ 38].
Proteomics is the combination of two-dimensional polyacrylamide gel electrophoresis (2D PAGE) for protein separation and visualization, followed by mass spectrometric (MS) protein identification using peptide mass fingerprints and tandem MS peptide sequencing [15].
We treated NPrEC with nitroso-cysteine and used the biotin switch technique followed by gel-based separation and mass spectrometry protein identification (using the LTQ-Orbitrap) to discover S-nitrosylated (SNO) proteins in the treated cells.
Subsequent protein identification using mass spectrometry gave rise to 15 unique proteins (Table 1).
Protein expression was confirmed with an anti-His-tag Western blot and peptide identification using mass spectrometry (Supplementary Figure S1).
We isolated spots/bands from 1D- (CCN2/CTGF) or 2D-gels (CCN3/NOV), subjected them to trypsin in-gel digesting and identified resulting peptides by ESI-TOF/MS and subsequent analysis using the MASCOT search engine (e.g. Table S1 and Table S2) for rapid protein identification using mass spectrometry data [37].
Protein identification using mass spectrometry is usually carried out by searching against databases of known proteins or transcripts.
Peptide identification using mass spectrometry is based on a simple principle where a peptide is ionized and the peptide bonds are fragmented in an MS-MS spectrometer.
In order to determine the antigens recognized by HCAb1 and HCAb2, immunoprecipitation of antigens followed by protein identification using mass spectrometry was performed.
PMMA IMERs with immobilized trypsin have shown enhanced enzyme stability, high reaction rates, and the absence of trypsin autodigestion, thereby simplifying protein identification using mass spectrometry.
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