1. Score filter for prey correlation: Only preys that pass this cutoff will be used for prey-prey correlation analysis. If a prey satisfies this cutoff for at least one bait, all quantitative values for this prey will be used across all baits, even those that did not satisfy the cutoff in particular bait-prey pairs.

2. Abundance cutoff for prey correlation (default 20): In addition to the above score filter requirement, a prey must have an abundance value above this parameter for at least one bait to be included in prey-prey correlation analysis. A high value helps to ensure that a prey is a suitably abundant protein easily detectable by the protocol and mass spectrometer used. This is prevents low abundance proteins from skewing the analysis. This parameter should be set to a lower value for small datasets.

3. Minimum bait requirement (default 1): Preys must pass the above filter and cutoff for this number of baits to be used in analysis. A higher cutoff prevents outlier baits from skewing the clustering.

4. Score filter for bait correlation: Only preys that pass this cutoff will be used for bait-bait correlation analysis. If a prey satisfies this cutoff for at least one bait, all quantitative values for this prey will be used across all baits, even those that did not satisfy the cutoff in particular bait-prey pairs. This should be set to a less stringent value than the cutoff for prey correlation to give more data points for correlation. As the number of baits and detected preys in the dataset increases, this parameter can be made more stringent, although this will be dataset dependent.

5. Abundance cutoff for bait correlation (default 20): In addition to the above filter requirement, a prey must have an abundance value above this parameter for at least one bait to be included in bait-bait correlation analysis.

6. Add back preys (default yes): If a prey passes the filter and minimum bait requirements described above then all data points for this prey across all baits will be included when performing the correlation.

7. Add bait counts (default no): SAINT automatically filters out peptides detected for the bait protein but this value can be simulated if this parameter is set to “yes”, in which case, the highest detected prey value satisfying the prey filter cutoff will be used for the bait. The absence of a bait gene can negatively affect correlation analysis for smaller clusters making it necessary in cases to simulate this value when not available.

8. Ignore source genes in correlation: (default no): By default all spectral count information is used when calculating the correlation between gene X and Y. However, there are cases when it may be appropriate to ignore spectral counts for the source genes (X and Y) themselves, particular when either gene was used as a bait. Setting this option to "yes" will cause the source gene spectral counts to be ignored during their pairwise correlation calculation.

9. Use replicates (default yes): If multiple enrichments/replicates have been performed for bait proteins, these replicates can be treated as separate entries for each bait when calculating the correlation or averaged to yield a single entry per bait. If replicates are present and this parameter is set to “yes”, replicates will be treated as separate entries for correlation. Replicate information must be specified as a pipe-separated list in the abundance column.

10. Control subtraction (default yes): The average value of a prey across control samples will be subtracted from the detected value for the bait if this is set to “yes”. The quantitative value for the prey becomes the value above and beyond what is seen across the control samples. Specify the column to use for controls in the adjacent "Control column" field.

11. Normalization (none by default): No normalization is applied by default, but when baits in the same dataset have been run on instruments with varying sensitivity or dynamic range, normalization should be applied. The options for normalization are to divide by the total abundance for all proteins identified in the run or normalize based on a specific prey. Normalization will be applied after control subtraction if both are specified.

12. Log transform (default no): If desired, data can be log-transformed by base 2, base 10 or natural. Log transformation will be performed after control subtraction and/or normalization if these are also specified.

13. Correlation cutoff for Cytoscape output (default 0.7): Text files compatible with direct input to Cytoscape (PMID:21149340) containing prey-prey and bait-bait pairs will be output from this tool to assist in generating network diagrams based on the prey-prey and bait-bait correlation profiles respectively. This parameter determines which gene pairs will be output, i.e. if a pair of genes has a correlation value above or equal to the default value of 0.7, it will be classified as an “interacting” pair and will be found in this file, and hence will have a connecting edge in Cytoscape. The text files will contain the gene pair and the correlation value.