Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023:2426:35-66.
doi: 10.1007/978-1-0716-1967-4_3.

Enhanced Proteomic Data Analysis with MetaMorpheus

Rachel M Miller  1 , Robert J Millikin  1 , Zach Rolfs  1 , Michael R Shortreed  1 , Lloyd M Smith  2
Affiliations

Enhanced Proteomic Data Analysis with MetaMorpheus

Rachel M Miller et al. Methods Mol Biol. 2023.

Abstract

MetaMorpheus is a free and open-source software program dedicated to the comprehensive analysis of proteomic data. In bottom-up proteomics, protein samples are digested into peptides prior to chromatographic separation and tandem mass spectrometric analysis. The resulting fragmentation spectra are subsequently analyzed with search software programs to obtain peptide identifications and infer the presence of proteins in the samples. MetaMorpheus seeks to maximize the information gleaned from proteomic data through the use of (a) mass calibration, (b) post-translational modification discovery, (c) multiple search algorithms, which aid in the analysis of data from traditional, crosslinking, and glycoproteomic experiments, (d) isotope-based or label-free quantification, (e) multi-protease protein inference, and (f) spectral annotation and data visualization capabilities. This protocol provides detailed descriptions of how use MetaMorpheus and how to customize data analysis workflows using MetaMorpheus tasks to meet the specific needs of the user.

Keywords: Bottom-up; Crosslink; Database search; Glycopeptides; Open-source; Post-translational modification discovery; Proteomics; Tandem mass spectrometry.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
MetaMorpheus application opens to the About window
Fig. 2
Fig. 2
Protein Databases window where users specify .FASTA or .XML databases for analysis
Fig. 3
Fig. 3
Spectra window where users specify spectra files for analysis
Fig. 4
Fig. 4
File-specific parameters window
Fig. 5
Fig. 5
Task window where users can add MetaMorpheus tasks to data analysis workflow
Fig. 6
Fig. 6
Run summary page containing all spectra files, databases, and tasks necessary for analysis with MetaMorpheus
Fig. 7
Fig. 7
PSM annotation window of MetaDraw within MetaMorpheus. A sample spectra annotation is displayed
Fig. 8
Fig. 8
Data Visualization window of MetaDraw within MetaMorpheus. A sample histogram of Precursor PPM errors is displayed
See this image and copyright information in PMC

References

    1. Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM, Yates JR (1999) Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol 17(7):676–682. 10.1038/10890 - DOI - PubMed
    1. Nesvizhskii AI (2010) A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics 73(11):2092–2123. 10.1016/j.jprot.2010.08.009 - DOI - PMC - PubMed
    1. Skinner OS, Kelleher NL (2015) Illuminating the dark matter of shotgun proteomics. Nat Biotechnol 33(7):717–718. 10.1038/nbt.3287 - DOI - PubMed
    1. Chick JM, Kolippakkam D, Nusinow DP, Zhai B, Rad R, Huttlin EL, Gygi SP (2015) A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides. Nat Biotechnol 33(7):743–749. 10.1038/nbt.3267 - DOI - PMC - PubMed
    1. Griss J, Perez-Riverol Y, Lewis S, Tabb DL, Dianes JA, Del-Toro N, Rurik M, Walzer M, Kohlbacher O, Hermjakob H, et al. (2016) Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets. Nate Methods 13(8):651–656. 10.1038/nmeth.3902 - DOI - PMC - PubMed

Publication types

LinkOut - more resources