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Crystal-C

A computational tool for refinement of open search results

Introduction

Open database search, which enlarges precursor tolerances (e.g. to 500 Da) to include more possible modified peptide candidates, is a practical and efficient approach for elucidating the “dark matter” of proteomics, including chemical and biological peptide modifications. Nevertheless, this strategy considers only unmodified peptide sequences during protein database search, resulting in large mass shifts between precursor neutral masses and identified peptide masses. These mass shifts may correspond to true post-translational modifications (PTMs) or artifacts from missed cleavages, in-source decay, and co-fragmentation (i.e., chimeric spectra). We hereby implemented a bioinformatics tool that detects and corrects possible artifacts, improving the interpretability of the open search results.

Parameters

How to Download

Download the latest version here

Commands

java -jar Crystal-C.jar Crystal-C.params PepXMLs

(For single pepXML)

java -Xmx8g -jar Crystal-C.jar Crystal-C.params test.pepXML

(For multiple pepXMLs)

java -Xmx8g -jar Crystal-C.jar Crystal-C.params *.pepXML