TIDD

TIDD is a universal post-processing tool which supports confident peptide identifications regardless of the search engine adopted. TIDD can work for any (including newly developed) search engines because it calculates universalfeatures that assess peptide-spectrum match quality while it allows additional featuresprovided by search engines (or users) as well.

Here, we support two types of TIDD version -- a simple GUI based TIDD and command version of TIDD

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Code download from Github: https://github.com/HanyangBISLab/TIDD.git

Download and test R&java code from R studio cloud: https://rstudio.cloud/spaces/178915/project/2994889

Test GUI from shinyapps.io: https://honglan-li.shinyapps.io/project/

<*This online GUI is just for testing, it may take very long time (or crash) to run real datasets becasuse of limited RAM/disk size, which supported by free R cloud studio. Therefore, we recommand you to run TIDD on local system.>

TIDD user manual files: https://docs.google.com/document/d/168oGySS15xrobeqTY54_QLMgWQofnPIApx6ma5ntGa8/edit?usp=sharing

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1. GUI

It is based on R and java programming.

So it required:

• install java jdk (17 or above) and R(4.1.2 or above)

• for R, the following packages are need to install.

  install.packages("shiny") install.packages("shinythemes") install.packages("shinyFiles") install.packages("shinydashboard") install.packages("ROCR") install.packages("e1071")

• run shinyApp

  PSM results:put psm result files to data/PSM/ mgf files: make a new dir. under data/MGF/ put mgf files to new dir.

Detail: TIDD: R and Java based program

1. install R version 4.1.2 (or above)

   link: https://cran.r-project.org/

   E.g. download R-4.1.2* ver

2. install R studio

link: https://www.rstudio.com/products/rstudio/download/

E.g. download Rstudio-2021.09.1*

3. install java 8

   download: https://www.oracle.com/java/technologies/downloads/ installation guide: https://docs.oracle.com/javase/10/install/installation-jdk-and-jre-microsoft-windows-platforms.htm#JSJIG-GUID-29333CFD-E7A6-498B-9317-97700C81D928

   E.g. jdk-17.01*

4. download TIDD code from git: https://github.com/HonglanLi/TIDD.git

5. unzip the TIDD*.zip

6. open the R studio

7. import TIDD project to R studio

   File --> Open project --> go to right position to select TIDD R project

                                   for example: "~/Download/TIDD-main/TIDD/TIDD.rproj
   

8. install R packages

   required packages: shiny, shinythemes, shinydashboard, shinyFiles, e1071, ROCR

   E.g. install shiny package

   console: install.packages("shiny")

   UI: click Packages --> install --> type "shiny" --> install

9 Run shinyAPP

open one of *R file in the TIDD rproject, and click "Run

2. commmand

• Extract TIDD features

  1. java -jar TIDD.jar < attributes>

  You can run "java -jar TIDD.jar -h" to check the options and their corresponding values

  (If you need to calculate XCorr, run "java -jar Xcorr_v2.jar " additionally)

  2. java -jar Xcorr_v2.jar < attributes>

  *detail: check usage (run java -jar Xcorr_v2.jar)

  3. run $Rscript TIDD_ModelFit.R
  • Change parameters inside the file: from line 30 to 41