Table 3.
Overview of MaxQuant output data evaluation with Perseus. The table lists the main steps of the Perseus analysis.
| No. | Command | Description |
|---|---|---|
| 1 | Generic matrix upload |
proteinGroups.txt normalized ratios, etc. |
| 2.1 | Filter rows based on categorical columns | Remove rows with “+” in reverse column |
| 2.2 | Remove rows with “+” in potential contaminant column | |
| 2.3 | Remove rows with “+” in only identified by site column | |
| 3 | Transform | Inverse ratios (1/x), ratios are reported as follows: ASC1 RPS2-birA*/birA* asc1− RPS2-birA*/birA* asc1− RPS2-birA*/ASC1 RPS2-birA* |
| 4 | Transform | log2(x) |
| 5 | Filter rows based on valid values | 9 valid values in total, Reduce matrix (431 proteins remained) |
| 6.1 | Categorical annotation rows |
Group biological replicates 1: ASC1 RPS2-birA*/birA* |
| 6.2 | 2: asc1− RPS2-birA*/birA* | |
| 6.3 | 3: asc1− RPS2-birA*/ASC1 RPS2-birA* | |
| 6.4 | 4: ASC1 RPS2-birA*/birA* and asc1− RPS2-birA*/birA* (for two sample t-test) | |
| 7.1 7.2 |
Two-sample tests | Select the two groups in 4 (see 6.4), p-value threshold: 0.05 p-value threshold: 0.01 |
| Filter for proteins enriched from ASC1 RPS2-birA* | ||
| 8 | Filter rows based on valid values | 3 valid values in group 1 greater than or equal to 0.485 (approximately 40% enrichment), reduce matrix |
| 9 | Average groups | Calculate mean and standard deviation |
| Filter for proteins enriched from asc1− RPS2-birA* but not from ASC1 RPS2-birA* | ||
| 10 | Filter rows based on valid values | 3 valid values in group 3 outside -0.485 and 0.485 Reduce matrix |
| 11 | Filter rows based on valid values | 3 valid values in group 2 greater than or equal to 0.485, Reduce matrix |
| 12 | Average groups | Calculate mean and standard deviation |