Table 1.
Overview of MS Results Obtained with MaxQuant Softwarea
| SILAC analysis | |
|---|---|
| proteins identifiedb | 2452 |
| proteins quantifiedc | 2045 |
| proteins differentially expressed following Cdc7 depletiond | 315 |
| significantly upregulated proteins | 145 |
| significantly downregulated proteins | 170 |
| number of MS full scans | 2034346 |
| number of MS/MS scan events | 647831 |
| number of MS/MS identified | 246220 |
| peptide sequences identified | 20950 |
| number of SILAC pairs | 234086 |
| number of SILAC pairs sequenced | 154648 (66.06%) |
| number of SILAC pairs identified | 87626 |
a
Shown are the results obtained by MaxQuant (version 1.0.13.13) analysis of the Cdc7-depleted SILAC data set using defined analysis parameters (outlined in the Experimental Section).
b
Protein groups identified under MaxQuant search parameters with protein and peptide FDR = 1%.
c
Protein abundance ratios are calculated as median values using a minimum of 3 quantifiable razor peptides.
d
Protein ratios with Significance B ≤ 0.05 were accepted as differentially expressed.