============================= RT-SVR (ver 2.0) DESCRIPTION ============================= In this version, Mascot Identity Threshold (MIT) is combined with RT-SVR so that all "good" peptide identifications will be obtained. ================ Download RT-SVR ================ RT-SVR (ver 2.0) is a Java executable application and supports most operation systems. It can be freely downloaded from http://pages.cs.wisc.edu/~yadi/bioinfo/rtsvr/rtsvr.html It is for research use only, permission is required for comercial use. ============================ Install and configure RT-SVR ============================ Unzip RT-SVR_2.0.zip and place the resulting RT-SVR folder in any location. In the folder, lib folder, Rc.txt and arff_title.txt cannot be modified or deleted. ================== How to run RT-SVR ================== To run RT-SVR correctly, three input files obtained from Mascot database search are needed. 1. Mascot target output for model construction (FDR=0.01) (See sample data file "FDR_0.01.csv): Run Mascot databases search at FDR=0.01, output the results file with .csv format (result.csv), include pep-score and pep-ident. Revise result.csv by deleting the column "prot-desc". In addition, split the column "pep_scan_title" by using "text-to-column" in Excel, create a column "RT/min" and put all retention times in this column. 2. Mascot target output for application (See sample data file "Target_p_0.10.csv): Run Mascot database search (target-decoy search) at some higher p value (e.g., p=0.10), output the target file in .csv format (target.csv), include pep-score and pep-ident. Revise target.csv by deleting the column "prot-desc". In addition, split the column "pep_scan_title" by using "text-to-column" in Excel, create a column "RT/min" and put all retention times in this column. 3. Mascot decoy output for application (See sample data file "Target_p_0.10.csv): When creating target output file shown above in (2), output the decoy file with .csv format (decoy.csv), include pep-score and pep-ident. Revise decoy.csv by deleting the column "prot-desc". In addition, split the column "pep_scan_title" by using "text-to-column" in Excel, create a column "RT/min" and put all retention times in this column. ======================== How to choose a q value ======================== q value is equivalent to FDR but more robust and confident. It is defined as the minimal FDR at which a peptide spectra match (PSM) can be accepted. In practice, each PSM will be calculated a corresponding q value. If a threshold for q value is set, all PSMs with larger q values than the threshold will be screened out. High threshold leads to more peptide predictions but low accuracy while small threshold increases accuracy but loses more PSMs. The default q value threshold is 0.01. Users can specify a different q value threshold based on the needs. A recommended range for q value threshold is [0, 0.10]. ============ Output file ============ In the output file, the predicted RT (shown as "Predicted"), RT error (shown as "Error") and q-value (shown as "q") will be appended as the last three columns (See "Target_p_0.10_rtsvr.csv"). The output file will be saved in the same directory as the input files. Check the information window for output file location when running RT-SVR. ========== Copyright ========== Author: Weifeng Cao, Yadi Ma Contact: wcao2@wisc.edu Copyright belongs to Li lab at University of Wisconsin-Madison. May 25, 2011.