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.
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References
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Acknowledgments
This work was supported by grant R35GM126914 from the National Institute of General Medical Sciences. R.J.M. was supported by an NHGRI training grant to the Genomic Sciences Training Program 5T32HG002760. We thank the software development team of the Smith Lab (Stefan K. Solntsev, Anthony J. Cesnik, Khairina Ibrahim, Lei Lu, Rachel M. Miller, Zach Rolfs, and Leah V. Schaffer), who contributed daily input and guidance for FlashLFQ’s improvement.
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Millikin, R.J., Shortreed, M.R., Scalf, M., Smith, L.M. (2023). Fast, Free, and Flexible Peptide and Protein Quantification with FlashLFQ. In: Burger, T. (eds) Statistical Analysis of Proteomic Data. Methods in Molecular Biology, vol 2426. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1967-4_13
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DOI: https://doi.org/10.1007/978-1-0716-1967-4_13
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Publisher Name: Humana, New York, NY
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Online ISBN: 978-1-0716-1967-4
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