The ESPPredictor module implements the enhanced signature peptide (ESP) predictor method developed by Fusaro et al. (2009). It provides a means of predicting, from sequence alone, which peptides for any given protein are likely to work well for targeted mass spec assay development.


How to run the module

Prerequisite: You will need a text file that contains a list of peptide sequences, one per line. The ESPPredictor module documentation describes one way of creating this list from protein sequences.

  1. Login to the public GenePattern server:
    If you do not have a GenePattern account, you can register on the login page.

    Result: GenePattern displays its main page.

  2. From the list of modules on the left, select the ESPPredictor module.
    Look for the module in the Proteomics category or select the All radio button to list the modules alphabetically.

    Result: GenePattern displays the ESPPredictor page.

  3. For the input file parameter, specify the list of peptide sequences.

    Result: GenePattern starts the job and displays the Job Status page.

  4. When the analysis completes, click the prediction.txt result file.

    Result: GenePattern displays the file, which lists each peptide sequence followed by the probability of its working well in the assay.


  • If an error occurs, check the input file. Typically, the error is due to (1) a non-standard amino acid J,U,Z,B,O,X in a sequence or (2) non-visible characters such as spaces or tabs before or after a sequence.
  • Depending on the number of peptide sequences the analysis may take a few seconds (<20 peptides) or many hours (>1,000 peptides). If you do not want to wait, you can continue working or exit from GenePattern. You can always find your jobs: (1) recent jobs are listed on the right side of the GenePattern main page or (2) click Job Results to see all jobs.