| Autor: |
Millikin RJ; Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States., Solntsev SK; Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States., Shortreed MR; Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States., Smith LM; Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States.; Genome Center of Wisconsin, University of Wisconsin , 425G Henry Mall, Room 3420, Madison, Wisconsin 53706, United States. |
| Abstrakt: |
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 following a search of bottom-up mass spectrometry data. FlashLFQ is approximately an order of magnitude faster than established label-free quantification methods. The increased speed makes it practical to base quantification upon all of the charge states for a given peptide rather than solely upon the charge state that was selected for MS2 fragmentation. This increases the number of quantified peptides, improves replicate-to-replicate reproducibility, and increases quantitative accuracy. We integrated FlashLFQ into the graphical user interface of the MetaMorpheus search software, allowing it to work together with the global post-translational modification discovery (G-PTM-D) engine to accurately quantify modified peptides. FlashLFQ is also available as a NuGet package, facilitating its integration into other software, and as a standalone command line software program for the quantification of search results from other programs (e.g., MaxQuant). |
