Missing value imputation options

Multiple imputation options were provided in FragPipe-Analyst. Perseus-style ** is applied by default for DDA and DIA LFQ data. No imputation is performed for TMT data by default.

• Perseus-style: This method is based on popular missing value imputation procedure implemented in Perseus software by MaxQuant team. The missing values are replaced by random numbers drawn from a normal distribution of 1.8 standard deviation down shift and with a width of 0.3 of each sample.
• knn: Missing values are replaced by nearest neighbor averaging technique.
• MLE: Maximum likelihood-based imputation method using the EM algorithm.
• min: Replaces the missing values by the smallest non-missing value in the data.
• zero: Replaces the missing values by 0.