Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine

Proteomics
David C GemperlineRichard D Vierstra

Abstract

Label-free quantitative MS based on the Normalized Spectral Abundance Factor (NSAF) has emerged as a straightforward and robust method to determine the relative abundance of individual proteins within complex mixtures. Here, we present Morpheus Spectral Counter (MSpC) as the first computational tool that directly calculates NSAF values from output obtained from Morpheus, a fast, open-source, peptide-MS/MS matching engine compatible with high-resolution accurate-mass instruments. NSAF has distinct advantages over other MS-based quantification methods, including a greater dynamic range as compared to isobaric tags, no requirement to align and re-extract MS1 peaks, and increased speed. MSpC features an easy-to-use graphic user interface that additionally calculates both distributed and unique NSAF values to permit analyses of both protein families and isoforms/proteoforms. MSpC determinations of protein concentration were linear over several orders of magnitude based on the analysis of several high-mass accuracy datasets either obtained from PRIDE or generated with total cell extracts spiked with purified Arabidopsis 20S proteasomes. The MSpC software was developed in C# and is open sourced under a permissive license with the code...Continue Reading

References

May 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·Scott A GerberSteven P Gygi
Sep 24, 2004·Molecular & Cellular Proteomics : MCP·Philip L RossDarryl J Pappin
Sep 2, 2006·Journal of Proteome Research·Boris ZybailovMichael P Washburn
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Jun 3, 2010·The Journal of Biological Chemistry·Adam J BookRichard D Vierstra
Jan 18, 2013·Journal of Proteome Research·Craig D Wenger, Joshua J Coon

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Citations

Sep 29, 2019·The Journal of Biological Chemistry·David C GemperlineRichard D Vierstra
Oct 28, 2019·Breast Cancer Research and Treatment·Nathan M MerrillMatthew B Soellner
Jul 7, 2019·Cellular and Molecular Life Sciences : CMLS·Severin MühlederWolfgang Holnthoner
Jul 30, 2020·Animals : an Open Access Journal From MDPI·Alicja Dratwa-ChałupnikAdelina Rogowska-Wrzesińska
Oct 24, 2019·Journal of the American Chemical Society·Yusheng XieHongyan Sun

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