Characterising phase variations in MALDI-TOF data and correcting them by peak alignment.

dc.contributor.author

Lin, Simon M

dc.contributor.author

Haney, Richard P

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Campa, Michael J

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Fitzgerald, Michael C

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Patz, Edward F

dc.coverage.spatial

United States

dc.date.accessioned

2016-02-01T14:50:45Z

dc.date.issued

2005

dc.description.abstract

The use of MALDI-TOF mass spectrometry as a means of analyzing the proteome has been evaluated extensively in recent years. One of the limitations of this technique that has impeded the development of robust data analysis algorithms is the variability in the location of protein ion signals along the x-axis. We studied technical variations of MALDI-TOF measurements in the context of proteomics profiling. By acquiring a benchmark data set with five replicates, we estimated 76% to 85% of the total variance is due to phase variation. We devised a lobster plot, so named because of the resemblance to a lobster claw, to help detect the phase variation in replicates. We also investigated a peak alignment algorithm to remove the phase variation. This operation is analogous to the normalization step in microarray data analysis. Only after this critical step can features of biological interest be clearly revealed. With the help of principal component analysis, we demonstrated that after peak alignment, the differences among replicates are reduced. We compared this approach to peak alignment with a model-based calibration approach in which there was known information about peaks in common among all spectra. Finally, we examined the potential value at each point in an analysis pipeline of having a set of methods available that includes parametric, semiparametric and nonparametric methods; among such methods are those that benefit from the use of prior information.

dc.identifier

http://www.ncbi.nlm.nih.gov/pubmed/19305630

dc.identifier.eissn

1176-9351

dc.identifier.uri

https://hdl.handle.net/10161/11570

dc.language

eng

dc.publisher

SAGE Publications

dc.relation.ispartof

Cancer Inform

dc.subject

MALDI-TOF

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amplitude

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peak alignment

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phase

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variation

dc.title

Characterising phase variations in MALDI-TOF data and correcting them by peak alignment.

dc.type

Journal article

duke.contributor.orcid

Fitzgerald, Michael C|0000-0002-6719-4722

duke.contributor.orcid

Patz, Edward F|0000-0003-3374-1596

pubs.author-url

http://www.ncbi.nlm.nih.gov/pubmed/19305630

pubs.begin-page

32

pubs.end-page

40

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Basic Science Departments

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Biochemistry

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Chemistry

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Clinical Science Departments

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Duke

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Duke Cancer Institute

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Institutes and Centers

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Pathology

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Pharmacology & Cancer Biology

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Radiology

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Radiology, Cardiothoracic Imaging

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School of Medicine

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Trinity College of Arts & Sciences

pubs.publication-status

Published

pubs.volume

1

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