| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T900 |
0-106 |
Sentence |
denotes |
When not explicitly indicated, we used defaults for MSstats for adjusted p values, even in cases of N = 2. |
| T901 |
107-240 |
Sentence |
denotes |
By default, MSstats uses Student’s t test for p value calculation and Benjamini-Hochberg method of FDR estimation to adjust p values. |
| T902 |
241-433 |
Sentence |
denotes |
Phosphorylation fold change data were filtered for quality based on consistency of observations between treatment and controls by requiring the MSstats reported value missingPercentage < 0.60. |
| T903 |
434-596 |
Sentence |
denotes |
This value is the proportion of features (i.e., peptide ions) that are missing across the treatment and control replicates for a specific fold change computation. |
| T904 |
597-685 |
Sentence |
denotes |
MSstats phosphorylation results had to be further simplified to effects at single sites. |
| T905 |
686-939 |
Sentence |
denotes |
The results of artMS/MSstats are fold changes of specific phosphorylation site groups detected within peptides, so one phosphorylation site can have multiple measurements if it occurs in different phosphorylation site groups (see Table S1 for examples). |
| T906 |
940-1189 |
Sentence |
denotes |
This complex dataset was reduced to a single fold change per site and time point by choosing (per time point) the fold change with the lowest p value, favoring those detected in both treatment and control, i.e., non-infinite log2 fold change values. |
| T907 |
1190-1325 |
Sentence |
denotes |
This single-site dataset, further reduced to those with human orthology (Table S1), was used as the input for kinase activity analysis. |
