A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles
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"A Proteome-wide, Quantitative Surve..." refers methods in this paper
...Ubiquitylated peptides were identified using MaxQuant....
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...Peptide Identification and Computational Analysis—Raw data files were analyzed using MaxQuant software (version 1.1.1.17) as described (29)....
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...Computational analysis was performed using MaxQuant (29), allowing a maximum false discovery rate of 1% at peptide and protein Proteome-wide Mapping of Endogenous Ubiquitylation Sites...
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...Peak lists were generated using MaxQuant (development version 1.0.14.3), and database searches were performed using Mascot search engine....
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...Site localization probabilities were determined by MaxQuant using PTM scoring algorithm as described previously (29, 31)....
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"A Proteome-wide, Quantitative Surve..." refers methods in this paper
...p values were calculated using nonpaired Wilcox test and adjusted for multiple comparisons (34)....
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"A Proteome-wide, Quantitative Surve..." refers methods in this paper
...For SILAC labeling, cells were cultured in media containing either L-arginine and L-lysine or L-arginine-U-(13)C6(15)N4 and L-lysine-U(13)C6(15)N2 (Cambridge Isotope Laboratories, Andover, MA) as described previously (20)....
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