skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Journal Article · · Proteomics
 [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
+ Show Author Affiliations

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/.

Research Organization:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences, and Biosciences Division
Grant/Contract Number:
FG02-88ER13968
OSTI ID:
1467443
Journal Information:
Proteomics, Vol. 16, Issue 6; ISSN 1615-9853
Publisher:
WileyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 5 works
Citation information provided by
Web of Science

References (16)

An Overview of Label-Free Quantitation Methods in Proteomics by Mass Spectrometry book December 2009
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ journal June 2014
Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics journal May 2002
Characterization and Quantification of Intact 26S Proteasome Proteins by Real-Time Measurement of Intrinsic Fluorescence Prior to Top-down Mass Spectrometry journal March 2013
Abacus: A computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis journal February 2011
Affinity Purification of the Arabidopsis 26 S Proteasome Reveals a Diverse Array of Plant Proteolytic Complexes journal June 2010
A guided tour of the Trans-Proteomic Pipeline journal January 2010
Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents journal September 2004
Tandem Mass Tags:  A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS journal April 2003
A Proteomics Search Algorithm Specifically Designed for High-Resolution Tandem Mass Spectra journal January 2013
Purification of the Arabidopsis 26 S Proteasome : BIOCHEMICAL AND MOLECULAR ANALYSES REVEALED THE PRESENCE OF MULTIPLE ISOFORMS journal November 2003
Detecting Differential and Correlated Protein Expression in Label-Free Shotgun Proteomics journal November 2006
Refinements to Label Free Proteome Quantitation: How to Deal with Peptides Shared by Multiple Proteins journal March 2010
Systematic Assessment of Survey Scan and MS2-Based Abundance Strategies for Label-Free Quantitative Proteomics Using High-Resolution MS Data journal March 2014
Statistical Analysis of Membrane Proteome Expression Changes in Saccharomyces c erevisiae journal September 2006
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS journal May 2003

Cited By (1)

Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in Arabidopsis journal September 2019

Similar Records

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Bioinformatics
Label-free quantification
LC-MS/MS
Morpheus
proteomics