Sample Run: Interactive Mode

Julio Marco Pineda edited this page Mar 21, 2018 · 7 revisions

Running Java files require using the JVM (Java Virtual Machine). The most common way to run JAR files uses the following commands in the command line:

java -jar <jar-file-name>.jar <arguments>

The jar-file-name for this program will be stability.jar. There are several arguments for stability.jar. For the interactive mode, here is the following to command to run:

java -jar stability.jar interactive

If you want to use the other mode please visit Input Mode.


Setting up peptide

  • For this part of the guide, we will save stability.jar in ~/test

  • Enter the following command: java -jar stability.jar interactive

  • Input the desired peptide sequence. For this guide, we will use a cyclic peptide with a disulfide linker: CGYEQDPWGVRYWYGCkkk(K-Biotin). Note that the program uses the character B for Biotin
  • The program prompts you of what type of peptide you will analyze. The current implementation has four types of peptides: linear, amide, DFBP, disulfide.

  • The program needs to know where the linker is connected to the peptide to form the cyclic connection. For our test peptide, the connection is in the 1st and 16th position. The program uses 0-index, thus we enter index 0 and index 15.
  • The program expects a list of the indices delimited by a comma. Thus, we enter 0,15
  • If you enter linear, the program will not prompt you for these indices.


This command of peptide-serum-stability allows you to enter mass spectrometry data and a threshold to determine the possible fragments in a serum stability study.

  • Enter the letter C. The program will now wait for mass spectrometry data input.

  • Enter the mass spectrometry measurement you want to check. We will use 1311.63 Daltons.
  • Enter the threshold to be used when comparing theoretical molecular weights to the input data. We will use 2.0 as a threshold.

  • If you want to try other data and/or thresholds, enter Y.
  • You can exit the (C)ompare command by entering, N.
  • To properly interpret the output of the program, especially suggested fragments with the # character, please visit Interpretation of Program Output.


This command of the peptide-serum-stability allows you to view the generated fragments from the input peptide given a certain length.

  • Enter P and enter the desired size. We will use fragment length of 5.

  • Once more, if you need guidance to interpret the format of the program output, please visit Interpretation of Program Output.
  • If you want to print other fragment sizes, enter Y.
  • You can exit the (P)rint command by entering, N.


To exit the program enter Q



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