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

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 higher 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. Lastly, the MSpC software was developed in C# and is open sourced under a permissive license with the code made available at http://dcgemperline.github.io/Morpheus_SpC/.

Authors:
 [1];  [2];  [2];  [3]
  1. Univ. of Wisconsin, Madison, WI (United States). Dept. of Genetics
  2. Univ. of Wisconsin, Madison, WI (United States). Dept. of Chemistry
  3. Univ. of Wisconsin, Madison, WI (United States). Dept. of Genetics; Washington Univ., St. Louis, MO (United States). Dept. of Biology
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Chemical Sciences, Geosciences & Biosciences Division
OSTI Identifier:
1467443
Grant/Contract Number:  
FG02-88ER13968
Resource Type:
Accepted Manuscript
Journal Name:
Proteomics
Additional Journal Information:
Journal Volume: 16; Journal Issue: 6; Journal ID: ISSN 1615-9853
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Bioinformatics; Label-free quantification; LC-MS/MS; Morpheus; proteomics

Citation Formats

Gemperline, David C., Scalf, Mark, Smith, Lloyd M., and Vierstra, Richard D. Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine. United States: N. p., 2016. Web. doi:10.1002/pmic.201500420.
Gemperline, David C., Scalf, Mark, Smith, Lloyd M., & Vierstra, Richard D. Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine. United States. doi:10.1002/pmic.201500420.
Gemperline, David C., Scalf, Mark, Smith, Lloyd M., and Vierstra, Richard D. Thu . "Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine". United States. doi:10.1002/pmic.201500420. https://www.osti.gov/servlets/purl/1467443.
@article{osti_1467443,
title = {Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine},
author = {Gemperline, David C. and Scalf, Mark and Smith, Lloyd M. and Vierstra, Richard D.},
abstractNote = {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 higher 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. Lastly, the MSpC software was developed in C# and is open sourced under a permissive license with the code made available at http://dcgemperline.github.io/Morpheus_SpC/.},
doi = {10.1002/pmic.201500420},
journal = {Proteomics},
number = 6,
volume = 16,
place = {United States},
year = {2016},
month = {1}
}

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