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Updated: Jun 12, 2026

Quantitative Analysis of Chromatin Proteomes in Disease
Published on: December 28, 2012
Label-Free Quantification in the Crux Toolkit
Frank Lawrence Nii Adoquaye Acquaye1,2, Bo Wen3, Charles E Grant3
1Department of Data Analysis and Artificial Intelligence and Laboratory on AI for Computational Biology, Faculty of Computer Science, HSE University, Moscow 109028, Russia.
None:
Ultimately, most tandem mass spectrometry (MS/MS) proteomics experiments aim to not just detect but also quantify the proteins in a given complex sample. Here, we describe an extension to the Crux MS/MS analysis toolkit to enable label-free quantification of peptides. We demonstrate that Crux's new quantification command, which is modeled after the algorithms implemented in the widely used FlashLFQ software, is both efficient and accurate. In particular, we achieve a 1.9-fold speedup while reducing the memory usage by 26%. The new crux-lfq command is available in Crux v5.0.
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