Computational protocol: Mass-Selected Site-SpecificCore-Fucosylation of Ceruloplasminin Alcohol-Related Hepatocellular Carcinoma

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Protocol publication

[…] The mass spectrum was searched with Proteome Discoverer 1.2 (Thermo Fisher Scientific, San Jose, CA) software with SEQUEST using the following settings: (1) fixed modification: cysteine carbamidomethylation (+57.0 Da); (2) dynamic modification: methionine oxidation (+16.0 Da), addition of GlcNAc (+203.1 Da), or GlcNAc+Fucose (+349.2 Da) to asparagine residue; (3) one missed cleavage was allowed; (4) peptide ion tolerance: 1.4 Da; (5) fragment ion tolerance: 0.8 Da; and (6) Swiss-Prot Homo sapiens database (release 2010_10, downloaded on Nov 2, 2010) was used.The identified target peptides were quantified manually with Xcalibur Qual Browser 2.1 (Thermo Fisher Scientific, San Jose, CA) using the peak area from the extracted ion chromatogram (XIC) with the following settings: (1) precursor peaks were extracted with a 1 Da (±0.5 Da) mass window, (2) scan filter was set as full MS, (3) boxcar-type of smoothing with 7 points was enabled, and (4) Genesis peak detection algorithm was used. […]

Pipeline specifications

Software tools Proteome Discoverer, Comet
Application MS-based untargeted proteomics
Organisms Homo sapiens, Hepatitis B virus, Hepacivirus C
Diseases Hepatitis B, Carcinoma, Hepatocellular, Liver Diseases
Chemicals Ethanol, Fucose