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Enhanced Proteomic Data Analysis with MetaMorpheus

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Statistical Analysis of Proteomic Data

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2426))

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.

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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. https://doi.org/10.1038/10890

  2. 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. https://doi.org/10.1016/j.jprot.2010.08.009

  3. Skinner OS, Kelleher NL (2015) Illuminating the dark matter of shotgun proteomics. Nat Biotechnol 33(7):717–718. https://doi.org/10.1038/nbt.3287

  4. 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. https://doi.org/10.1038/nbt.3267

  5. 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. https://doi.org/10.1038/nmeth.3902

  6. Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R (2006) Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol Cell Proteom 5(4):652–670. https://doi.org/10.1074/mcp.M500319-MCP200

  7. Solntsev SK, Shortreed MR, Frey BL, Smith LM (2018) Enhanced global post-translational modification discovery with metamorpheus. J Proteome Res 17(5):1844–1851. https://doi.org/10.1021/acs.jproteome.7b00873

  8. Lu L, Millikin RJ, Solntsev SK, Rolfs Z, Scalf M, Shortreed MR, Smith LM (2018) Identification of MS-cleavable and noncleavable chemically cross-linked peptides with metamorpheus. J Proteome Res 17(7):2370–2376. https://doi.org/10.1021/acs.jproteome.8b00141

  9. Lu L, Riley NM, Shortreed MR, Bertozzi CR, Smith LM (2020) O-pair search with metamorpheus for o-glycopeptide characterization. bioRxiv https://doi.org/10.1101/2020.05.18.102327

  10. Millikin RJ, Solntsev SK, Shortreed MR, Smith LM (2018) Ultrafast peptide label-free quantification with FlashLFQ. J Proteome Res 17(1):386–391. https://doi.org/10.1021/acs.jproteome.7b00608

  11. Miller RM, Millikin RJ, Hoffmann CV, Solntsev SK, Sheynkman GM, Shortreed MR, Smith LM (2019) Improved protein inference from multiple protease bottom-up mass spectrometry data. J Proteome Res 18(9):3429–3438. https://doi.org/10.1021/acs.jproteome.9b00330

  12. Kong AT, Leprevost FV, Avtonomov DM, Mellacheruvu D, Nesvizhskii AI (2017) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14(5):513–520. https://doi.org/10.1038/nmeth.4256

  13. Cesnik AJ, Miller RM, Ibrahim K, Lu L, Millikin RJ, Shortreed MR, Frey BL, Smith LM (2020) Spritz: A proteogenomic database engine. bioRxiv https://doi.org/10.1101/2020.06.08.140681

  14. Giansanti P, Tsiatsiani L, Low TY, Heck AJ (2016) Six alternative proteases for mass spectrometry–based proteomics beyond trypsin. Nat Protocols 11(5):993–1006. https://doi.org/10.1038/nprot.2016.057

  15. Varki A (1993) Biological roles of oligosaccharides: all of the theories are correct. Glycobiology 3(2):97–130. https://doi.org/10.1093/glycob/3.2.97

  16. Gupta N, Pevzner PA (2009) False discovery rates of protein identifications: a strike against the two-peptide rule. J Proteome Res 8(9):4173–4181. https://doi.org/10.1021/pr9004794

  17. Dai Y, Buxton KE, Schaffer LV, Miller RM, Millikin RJ, Scalf M, Frey BL, Shortreed MR, Smith LM (2019) Constructing human proteoform families using intact-mass and top-down proteomics with a multi-protease global post-translational modification discovery database. J Proteome Res 18(10):3671–3680. https://doi.org/10.1021/acs.jproteome.9b00339

  18. Howbert JJ, Noble WS (2014) Computing exact p-values for a cross-correlation shotgun proteomics score function. Mol Cell Proteom 13(9):2467–2479. https://doi.org/10.1074/mcp.O113.036327

  19. Rolfs Z, Millikin RJ, Smith LM (2020) An algorithm to improve the speed of semi- and non-specific enzyme searches in proteomics. Curr Bioinf 15:1–9. https://doi.org/10.2174/1574893615999200429123334

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Acknowledgements

The development and maintenance of MetaMorpheus is supported by NIH-NIGMS grant R35GM126914. Rachel M. Miller was supported in part by the NIH Chemistry-Biology Interface Training Grant (T32GM008505). Robert J. Millikin was supported by the NIH Genomic Sciences Training Program (5T32HG002760). Zach Rolfs was supported by NIH-NCI grant U24CA199347.

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Authors and Affiliations

  1. University of Wisconsin-Madison, Department of Chemistry, Madison, WI, USA

    Rachel M. Miller, Robert J. Millikin, Zach Rolfs, Michael R. Shortreed & Lloyd M. Smith

Authors
  1. Rachel M. Miller
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  2. Robert J. Millikin
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  3. Zach Rolfs
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  4. Michael R. Shortreed
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  5. Lloyd M. Smith
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Corresponding author

Correspondence to Lloyd M. Smith .

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Editors and Affiliations

  1. Exploring the Dynamics of Proteomes, Proteomics French Infrastructure, Université Grenoble Alpes, CNRS, CEA, INSERM, Grenoble, France

    Thomas Burger

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Miller, R.M., Millikin, R.J., Rolfs, Z., Shortreed, M.R., Smith, L.M. (2023). Enhanced Proteomic Data Analysis with MetaMorpheus. In: Burger, T. (eds) Statistical Analysis of Proteomic Data. Methods in Molecular Biology, vol 2426. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1967-4_3

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  • DOI: https://doi.org/10.1007/978-1-0716-1967-4_3

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1966-7

  • Online ISBN: 978-1-0716-1967-4

  • eBook Packages: Springer Protocols

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