SHIFTS

SHIFTS (Systematic, Hypothesis-free Identification of PTMs with controlled FDR based on ultra-Tolerant database search) is a program made in the Jesús Vázquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares (CNIC), for high throughput PTM (Post translation modifications) processing.

SHIFTS identifies peaks in the Delta Mass distribution, assigns PSM to peaks and calculates FDR for peptide identification. SHIFTS is developed in python programming language as command line tool and its works with cometPTM produced ".txt" files.

Installation

Prerequisites

Before you begin, ensure you have met the following requirements:

• You have Python installed on your machine. You can download it from python.org.

Setting Up the Python Environment

To set up the Python environment and install the required packages, follow these steps:

1. Create a virtual environment

python -m venv env

2. Activate the virtual environment and install the dependencies

source env/bin/activate && pip install -r python_requirements.txt

Usage

For information on using several programs, you can consult the USAGE.md file.