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Mass mapping of tryptic fragments further verified its identity.
β1,4 galactosidase treatment showed the structural difference was the absence of the penultimate Gal from the biantennary oligosaccharides, and mapping of tryptic glycopeptides confirmed these results showing that approximately half the chains lacked Gal.
The generation of tryptic fragments from detergent phase-fractionated proteins of Mcc Kid, LC-MS/MS techniques and mapping of tryptic peptides to ORFs encoded by the Mcc Kid genome sequence have been described in detail elsewhere [ 43].
Mass mapping of tryptic peptides was performed using MALDI-TOF (above protocol) or Cap-LC-MS/MS on Micromass Q-TOF Ultima mass spectrometer with LC-packings pep Map C18, 75 μm ID column using a gradient of 7 80%95%5% acetonitrile and 0.1% formic acid) over a period of 35 min.
2D peptide mapping of tryptic peptides from autophosphorylated eEF2K preparations radiolabelled in vitro was carried out as described previously [ 30], except that detection was by autoradiography and digestion was performed using trypsin in the presence of the reducing agent tris 2-carboxyethyl phosphine atris 2-carboxyethyl phosphinemM.
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Peptide mapping of the tryptic digest identified it as complement component 3 precursor (estimated Z-score 1.57, 4% sequence coverage).
Two-dimensional peptide mapping and amino acid analysis of tryptic peptides from the phosphorylated protein (data not shown) suggested a single major site of phosphorylation at the serine within the sequence RTPSGK at amino acids 95 100.
To identify the 135-kDa protein detected in the UV cross-linking assays), the corresponding protein band was excised from the duplicate CBB-stained gel and prepared for MS analysis by tryptic mapping of the 135-kDa protein band by MALDI-TOF-MS, MS/MS and de novo sequencing.
Peptide maps of FVII-isolates were generated by chromatographic separation of tryptic peptides, and subsequent mass spectrometric analysis enabled relative quantification of γ-carboxylation, β-hydroxylation, and of N-linked and O-linked glycans.
Despite the fact that capillary electrophoresis (CE) has been shown to be a powerful tool for the separation and detection of tryptic peptide fragments after protein digestion, this technique lacks sensitivity for mapping proteins isolated in very small quantities from biological samples.
The use of tryptic digestion-RPLC showed identical digestion patterns between SEC and batch refolded u-PA.
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