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Proteoform Analysis and Construction of Proteoform Families in Proteoform Suite

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Proteoform Identification

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2500))

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Abstract

Proteoform Suite is an interactive software program for the identification and quantification of intact proteoforms from mass spectrometry data. Proteoform Suite identifies proteoforms observed by intact-mass (MS1) analysis. In intact-mass analysis, unfragmented experimental proteoforms are compared to a database of known proteoform sequences and to one another, searching for mass differences corresponding to well-known post-translational modifications or amino acids. Intact-mass analysis enables proteoforms observed in the MS1 data without MS/MS (MS2) fragmentation to be identified. Proteoform Suite further facilitates the construction and visualization of proteoform families, which are the sets of proteoforms derived from individual genes. Bottom-up peptide identifications and top-down (MS2) proteoform identifications can be integrated into the Proteoform Suite analysis to increase the sensitivity and accuracy of the analysis. Proteoform Suite is open source and freely available at https://github.com/smith-chem-wisc/proteoform-suite.

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References

  1. Smith LM, Kelleher NL, Consortium for Top Down Proteomics (2013) Proteoform: a single term describing protein complexity. Nat Methods 10(3):186–187. https://doi.org/10.1038/nmeth.2369

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Shortreed MR, Frey BL, Scalf M, Knoener RA, Cesnik AJ, Smith LM (2016) Elucidating proteoform families from proteoform intact-mass and lysine-count measurements. J Proteome Res 15(4):1213–1221. https://doi.org/10.1021/acs.jproteome.5b01090

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Cai W, Tucholski TM, Gregorich ZR, Ge Y (2016) Top-down proteomics: technology advancements and applications to heart diseases. Expert Rev Proteomics 13(8):717–730. https://doi.org/10.1080/14789450.2016.1209414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Chen B, Brown KA, Lin Z, Ge Y (2018) Top-down proteomics: ready for prime time? Anal Chem 90(1):110–127. https://doi.org/10.1021/acs.analchem.7b04747

    Article  CAS  PubMed  Google Scholar 

  5. Toby TK, Fornelli L, Kelleher NL (2016) Progress in top-down proteomics and the analysis of proteoforms. Annu Rev Anal Chem (Palo Alto, Calif) 9(1):499–519. https://doi.org/10.1146/annurev-anchem-071015-041550

    Article  CAS  Google Scholar 

  6. Cesnik AJ, Shortreed MR, Schaffer LV, Knoener RA, Frey BL, Scalf M, Solntsev SK, Dai Y, Gasch AP, Smith LM (2018) Proteoform Suite: software for constructing, quantifying, and visualizing proteoform families. J Proteome Res 17(1):568–578. https://doi.org/10.1021/acs.jproteome.7b00685

    Article  CAS  PubMed  Google Scholar 

  7. Schaffer LV, Shortreed MR, Cesnik AJ, Frey BL, Solntsev SK, Scalf M, Smith LM (2018) Expanding proteoform identifications in top-down proteomic analyses by constructing proteoform families. Anal Chem 90(2):1325–1333. https://doi.org/10.1021/acs.analchem.7b04221

    Article  CAS  PubMed  Google Scholar 

  8. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504. https://doi.org/10.1101/gr.1239303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27(3):431–432. https://doi.org/10.1093/bioinformatics/btq675

    Article  CAS  PubMed  Google Scholar 

  10. Toby TK, Fornelli L, Kristina S, DeHart CJ, Fellers RT (2019) A comprehensive pipeline for translational top-down proteomics from a single blood draw. Nat Protoc 14:119–152. https://doi.org/10.1038/s41596-018-0085-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Donnelly DP, Rawlins CM, DeHart CJ, Fornelli L, Schachner LF, Lin Z, Lippens JL, Aluri KC, Sarin R, Chen B, Lantz C, Jung W, Johnson KR, Koller A, Wolff JJ, Campuzano IDG, Auclair JR, Ivanov AR, Whitelegge JP, Pasa-Tolic L, Chamot-Rooke J, Danis PO, Smith LM, Tsybin YO, Loo JA, Ge Y, Kelleher NL, Agar JN (2019) Best practices and benchmarks for intact protein analysis for top-down mass spectrometry. Nat Methods 16(7):587–594. https://doi.org/10.1038/s41592-019-0457-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Jeong K, Kim J, Gaikwad M, Hidayah SN, Heikaus L, Schluter H, Kohlbacher O (2020) FLASHDeconv: ultrafast, high-quality feature deconvolution for top-down proteomics. Cell Syst 10(2):213–218 e216. https://doi.org/10.1016/j.cels.2020.01.003

    Article  CAS  PubMed  Google Scholar 

  13. Dai Y, Shortreed MR, Scalf M, Frey BL, Cesnik AJ, Solntsev S, Schaffer LV, Smith LM (2017) Elucidating Escherichia coli proteoform families using intact-mass proteomics and a global PTM discovery database. J Proteome Res 16(11):4156–4165. https://doi.org/10.1021/acs.jproteome.7b00516

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Li Q, Shortreed MR, Wenger CD, Frey BL, Schaffer LV, Scalf M, Smith LM (2017) Global post-translational modification discovery. J Proteome Res 16(4):1383–1390. https://doi.org/10.1021/acs.jproteome.6b00034

    Article  CAS  PubMed  Google Scholar 

  16. LeDuc RD, Fellers RT, Early BP, Greer JB, Thomas PM, Kelleher NL (2014) The C-score: a Bayesian framework to sharply improve proteoform scoring in high-throughput top down proteomics. J Proteome Res 13(7):3231–3240. https://doi.org/10.1021/pr401277r

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. 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

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported by the National Institute of General Medical Sciences of the National Institutes of Health (NIH) under Award Number R35GM126914. LVS was supported by the NIH Biotechnology Training Program, T32GM008349.

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Authors and Affiliations

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

    Leah V. Schaffer, Michael R. Shortreed & Lloyd M. Smith

Authors
  1. Leah V. Schaffer
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  2. Michael R. Shortreed
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  3. Lloyd M. Smith
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Corresponding author

Correspondence to Lloyd M. Smith .

Editor information

Editors and Affiliations

  1. Department of Chemistry, Michigan State University, East Lansing, MI, USA

    Liangliang Sun

  2. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA

    Xiaowen Liu

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Schaffer, L.V., Shortreed, M.R., Smith, L.M. (2022). Proteoform Analysis and Construction of Proteoform Families in Proteoform Suite. In: Sun, L., Liu, X. (eds) Proteoform Identification. Methods in Molecular Biology, vol 2500. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2325-1_7

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  • DOI: https://doi.org/10.1007/978-1-0716-2325-1_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2324-4

  • Online ISBN: 978-1-0716-2325-1

  • eBook Packages: Springer Protocols

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