Fast, Free, and Flexible Peptide and Protein Quantification with FlashLFQ

Robert J Millikin; Michael R Shortreed; Mark Scalf; Lloyd M Smith

doi:10.1007/978-1-0716-1967-4_13

Fast, Free, and Flexible Peptide and Protein Quantification with FlashLFQ

Methods Mol Biol. 2023:2426:303-313. doi: 10.1007/978-1-0716-1967-4_13.

Authors

Robert J Millikin¹, Michael R Shortreed¹, Mark Scalf¹, Lloyd M Smith²

Affiliations

¹ Department of Chemistry, University of Wisconsin, Madison, WI, USA.
² Department of Chemistry, University of Wisconsin, Madison, WI, USA. smith@chem.wisc.edu.

Abstract

The rapid and accurate quantification of peptides is a critical element of modern proteomics that has become increasingly challenging as proteomic data sets grow in size and complexity. We present here FlashLFQ, a computer program for high-speed label-free quantification of peptides and proteins following a search of bottom-up mass spectrometry data. FlashLFQ is approximately an order of magnitude faster than established label-free quantification methods and can quantify data-dependent analysis (DDA) search results from any proteomics search program. It is available as a graphical user interface program, a command line tool, a Docker image, and integrated into the MetaMorpheus search software.

Keywords: Label-free quantification; Post-translational modifications; Quantitative proteomics; Software.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Mass Spectrometry / methods
Peptides / chemistry
Proteins* / chemistry
Proteomics* / methods
Software

Substances

Proteins
Peptides

Abstract

Publication types

MeSH terms

Substances

Grants and funding