| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T889 |
0-106 |
Sentence |
denotes |
Quantitative analysis was performed in the R statistical programming language (version 3.6.1, 2019-07-05). |
| T890 |
107-318 |
Sentence |
denotes |
Initial quality control analyses, including inter-run clusterings, correlations, principal components analysis, peptide and protein counts and intensities were completed with the R package artMS (version 1.5.3). |
| T891 |
319-513 |
Sentence |
denotes |
Based on obvious outliers in intensities, correlations, and clusterings, 2 runs were discarded from the protein abundance data and 2 runs were discarded from the phosphopeptide data (Figure S1). |
| T892 |
514-790 |
Sentence |
denotes |
Additionally, the phosphopeptide data were filtered based on feature (i.e., peptide ion) intensity, removing any single feature with intensity less than 214—this decision was made based on apparent lack of correlation between runs for feature intensities below this intensity. |
| T893 |
791-1122 |
Sentence |
denotes |
Thus, for both phosphopeptides and protein abundance, we had 2 control time points and 6 infected time points, each with 3 biologically distinct replicates, except for infected at 0 and 2 hours in the phosphopeptide data and control at 0 hours and infected at 0 hours in the protein abundance data which only had 2 replicates each. |
