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pmic7244-sup-0001-figureS1.doc214KFigure S1 Venn diagrams showing the overlapping and unique data of three runs of analyses. (A) 193 glycoproteins (RSD=2.1%, n=3) were identified in each run of three replicate runs of 1D LC-MS/MS in first biological replicate and more than 65% of total identified proteins in three runs can be identified in two or three runs. (B) 208 glycoproteins (RSD=5.5%, n=3) were identified in each run of three replicate runs of 1D LC-MS/MS in another biological replicate and more than 70% of total identified proteins in three runs can be identified in two or three runs. (C) 458 unique glycopeptides (RSD=2.4%, n=3) were identified in each run of three replicate runs of 1D LC-MS/MS in first biological replicate. (D) 508 unique glycopeptides (RSD=5.7%, n=3) were identified in each run of three replicate runs of 1D LC-MS/MS in another biological replicate. (E) 5379 unique tryptic peptides (RSD=10.4%, n=3) were identified in each run of three replicate runs of 2D LC-MS/MS in first biological replicate. (F) 5084 unique tryptic peptides (RSD=14.9%, n=3) were identified in each run of three replicate runs of 2D LC-MS/MS in another biological replicate.
pmic7244-sup-0002-tableS1.xlsx4477KTable S1. The detailed information about the identified glycopeptides, N-glycosites and glycoproteins in first biological replicate.
pmic7244-sup-0003-tableS2.xlsx4724KTable S2. The detailed information about the identified glycopeptides, N-glycosites and glycoproteins in another biological replicate.
pmic7244-sup-0004-tableS3.xlsx12KTable S3. List of CD-annotated proteins among the identified glycoproteins
pmic7244-sup-0005-tableS4.xlsx27KTable S4. The detailed information about the isotopic labelled glycopeptides from both HepG2 and Chang Liver cell lines in two technical replicates. (The released non-glycopeptides and glycopeptides from Chang Liver and HepG2 cells were all labelled with light and heavy dimethyl, respectively, by an in-solution stable isotope dimethyl labelling approach)
pmic7244-sup-0006-tableS5.xlsx69KTable S5. List of confidentially identified proteins in the control experiment of differential analysis of cell surface glycoproteins between two HepG2 cells (criterion: the protein should be identified by at least two unique non-glycopeptides with the RSD < 1 in each LC-MS/MS analysis and should be identified in at least two LC-MS/MS analysis.)
pmic7244-sup-0007-tableS6.xlsx36KTable S6. List of confidentially identified proteins in first biological replicate (criterion: the protein should be identified by at least two unique non-glycopeptides with the RSD<1 in each LC-MS/MS analysis and should be identified in at least two LC-MS/MS analysis.)
pmic7244-sup-0008-tableS7.xlsx35KTable S7. List of confidentially identified proteins in another biological replicate (criterion: the protein should be identified by at least two unique non-glycopeptides with the RSD<1 in each LC-MS/MS analysis and should be identified in at least two LC-MS/MS analysis.)
pmic7244-sup-0009-tableS8.xlsx14KTable S8. List of confidentially identified proteins with significant expression change (dimethyl labelled non-glycopeptide ratio of HepG2/CL >2 or <0.5) in two biological replicates
pmic7244-sup-0010-tableS9.xlsx47KTable S9. The detailed information about the isotopic labelled glycopeptides from both HepG2 and Chang Liver cell lines in two technical replicates. (The enrichment was performed on the peptide level)

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