Skip to main content
SpringerLink
Log in

Computer-Assisted Data Processing, Analysis and Mining for New Applications

  • Chapter
  • First Online:
Mass Spectrometry: Developmental Approaches to Answer Biological Questions

Part of the book series: SpringerBriefs in Bioengineering ((BRIEFSBIOENG))

  • 1306 Accesses

Abstract

The development of new mass spectrometry-based methods provides sets of data that need to be processed in order to extract the information of interest. Considering that the amount of data produced is humanly manageable, a one-off experiment may be processed manually. However, when the amount of data cannot be managed manually or once the method has to be used at high throughput, it becomes necessary to develop computer-based data processing. Large sets of data also require computer assistance for statistical analysis for example. In general, computer processing reduces the time necessary for the analysis and allows the management of large sets of data. The current chapter presents the development of software and computer assisted method for the processing of mass spectrometry data associated with newly developed methods.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Stoeckli M, Farmer TB, Caprioli RM. Automated mass spectrometry imaging with a matrix-assisted laser desorption ionization time-of-flight instrument. J Am Soc Mass Spectrom. 1999;10(1):67–71.

    Article  CAS  Google Scholar 

  2. proteowizard.sourceforge.net http://proteowizard.sourceforge.net

  3. world-2dpage.expasy.org http://world-2dpage.expasy.org

  4. www.maxquant.org http://www.maxquant.org

  5. http://www.matrixscience.com/search_form_select.html

  6. premierbiosoft.com http://premierbiosoft.com

  7. www.maldi-msi.org http://www.maldi-msi.org

  8. Trim PJ, Djidja MC, Muharib T, Cole LM, Flinders B, Carolan VA, Francese S, Clench MR. Instrumentation and software for mass spectrometry imaging-making the most of what you’ve got. J Proteomics. 2012;75(16):4931–40.

    Article  CAS  Google Scholar 

  9. Pascal BD, Willis S, Lauer JL, Landgraf RR, West GM, Marciano D, Novick S, Goswami D, Chalmers MJ, Griffin PR. HDX workbench: software for the analysis of H/D exchange MS data. J Am Soc Mass Spectrom. 2012;23(9):1512–21.

    Article  CAS  Google Scholar 

  10. Pascal BD, Chalmers MJ, Busby SA, Griffin PR. HD desktop: an integrated platform for the analysis and visualization of H/D exchange data. J Am Soc Mass Spectrom. 2009;20(4):601–10.

    Article  CAS  Google Scholar 

  11. Nikamanon P, Pun E, Chou W, Koter MD, Gershon PD. "TOF2H": a precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis. BMC Bioinform. 2008;9:387.

    Article  Google Scholar 

  12. Liu S, Liu L, Uzuner U, Zhou X, Gu M, Shi W, Zhang Y, Dai SY, Yuan JS. HDX-analyzer: a novel package for statistical analysis of protein structure dynamics. BMC Bioinform. 2011;12 (Suppl 1):43

    Article  Google Scholar 

  13. Zhang Z, Zhang A, Xiao G. Improved protein hydrogen/deuterium exchange mass spectrometry platform with fully automated data processing. Anal Chem. 2012;84(11):4942–9.

    Google Scholar 

  14. Venable JD, Scuba W, Brock A. Feature based retention time alignment for improved HDX MS analysis. J Am Soc Mass Spectrom. 2013;24(4):642–5.

    Google Scholar 

  15. Kan ZY, Walters BT, Mayne L, Englander SW. Protein hydrogen exchange at residue resolution by proteolytic fragmentation mass spectrometry analysis. Proc Natl Acad Sci U S A. 2013;110(41):16438–43.

    Google Scholar 

  16. Schilling B, Row RH, Gibson BW, Guo X, Young MM. MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides. J Am Soc Mass Spectrom. 2003;14(8):834–50.

    Article  CAS  Google Scholar 

  17. Tang Y, Chen Y, Lichti CF, Hall RA, Raney KD, Jennings SF. CLPM: a cross-linked peptide mapping algorithm for mass spectrometric analysis. BMC Bioinform. 2005;6 Suppl 2:S9

    Google Scholar 

  18. Götze M, Pettelkau J, Schaks S, Bosse K, Ihling CH, Krauth F, Fritzsche R, Kühn U, Sinz A. StavroX-a software for analyzing crosslinked products in protein interaction studies. J Am Soc Mass Spectrom. 2012;23(1):76–87.

    Article  Google Scholar 

  19. Söderberg CA, Lambert W, Kjellström S, Wiegandt A, Wulff RP, Månsson C, Rutsdottir G, Emanuelsson C. Detection of crosslinks within and between proteins by LC-MALDI-TOFTOF and the software FINDX to reduce the MSMS-data to acquire for validation. PLoS ONE. 2012;7(6):e38927.

    Article  Google Scholar 

  20. Holding AN, Lamers MH, Stephens E, Skehel JM. Hekate: software suite for the mass spectrometric analysis and three-dimensional visualization of cross-linked protein samples. J Proteome Res. 2013;12(12):5923–33.

    Article  CAS  Google Scholar 

  21. Olsen JV, Mann M. Status of large-scale analysis of post-translational modifications by mass spectrometry. Mol Cell Proteomics. 2013;12(12):3444–52.

    Article  CAS  Google Scholar 

  22. Na S, Paek E. Software eyes for protein post-translational modifications. Mass Spectrom Rev. 2014 Jun 2. doi:10.1002/mas.21425.

    Google Scholar 

  23. Serang O, Froehlich JW, Muntel J, McDowell G, Steen H, Lee RS, Steen JA. SweetSEQer, simple de novo filtering and annotation of glycoconjugate mass spectra. Mol Cell Proteomics. 2013;12(6):1735–40.

    Article  CAS  Google Scholar 

  24. Zhu Z, Hua D, Clark DF, Go EP, Desaire H. GlycoPep Detector: a tool for assigning mass spectrometry data of N-linked glycopeptides on the basis of their electron transfer dissociation spectra. Anal Chem. 2013;85(10):5023–32.

    Article  CAS  Google Scholar 

  25. Zhu Z, Su X, Clark DF, Go EP, Desaire H. Characterizing O-linked glycopeptides by electron transfer dissociation: fragmentation rules and applications in data analysis. Anal Chem. 2013;85(17):8403–11.

    Article  CAS  Google Scholar 

  26. Yu CY, Mayampurath A, Hu Y, Zhou S, Mechref Y, Tang H. Automated annotation and quantification of glycans using liquid chromatography-mass spectrometry. Bioinformatics. 2013;29(13):1706–7.

    Article  CAS  Google Scholar 

  27. Kronewitter SR, Slysz GW, Marginean I, Hagler CD, LaMarche BL, Zhao R, Harris MY, Monroe ME, Polyukh CA, Crowell KL, Fillmore TL, Carlson TS, Camp DG 2nd, Moore RJ, Payne SH, Anderson GA, Smith RD. GlyQ-IQ: Glycomics Quintavariate-Informed Quantification with High-Performance Computing and GlycoGrid 4D Visualization. Anal Chem. 2014;86(13):6268–76.

    Article  CAS  Google Scholar 

  28. Campbell MP, Ranzinger R, Lütteke T, Mariethoz J, Hayes CA, Zhang J, Akune Y, Aoki-Kinoshita KF, Damerell D, Carta G, York WS, Haslam SM, Narimatsu H, Rudd PM, Karlsson NG, Packer NH, Lisacek F. Toolboxes for a standardised and systematic study of glycans. BMC Bioinform. 2014;15(Suppl 1):S9.

    Article  Google Scholar 

  29. Park HM, Park JH, Kim YW, Kim KJ, Jeong HJ, Jang KS, Kim BG, Kim YG. The Xeno-glycomics database (XDB): a relational database of qualitative and quantitative pig glycome repertoire. Bioinformatics. 2013;29(22):2950–2.

    Article  CAS  Google Scholar 

  30. www.ms-utils.org http://www.ms-utils.org

Download references

Author information

Authors and Affiliations

  1. PDRA, Pharmacology Department, University of Oxford, Oxford, United Kingdom

    Gwenael Pottiez

Authors
  1. Gwenael Pottiez
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gwenael Pottiez .

Rights and permissions

Reprints and permissions

Copyright information

© 2015 The Author

About this chapter

Cite this chapter

Pottiez, G. (2015). Computer-Assisted Data Processing, Analysis and Mining for New Applications. In: Mass Spectrometry: Developmental Approaches to Answer Biological Questions. SpringerBriefs in Bioengineering. Springer, Cham. https://doi.org/10.1007/978-3-319-13087-3_7

Download citation

Publish with us

Policies and ethics

Search

Navigation