Improved parametric time warping for proteomics

TG Bloemberg; J Gerretzen; HJP Wouters; J Gloerich; M van Dael; HJCT Wessels; LP van den Heuvel; Paul Eilers; LMC Buydens; Rik Wehrens

doi:10.1016/j.chemolab.2010.04.008

Improved parametric time warping for proteomics

TG Bloemberg, J Gerretzen, HJP Wouters, J Gloerich, M van Dael, HJCT Wessels, LP van den Heuvel, Paul Eilers, LMC Buydens, Rik Wehrens

Research output: Contribution to journal › Article › Academic › peer-review

68 Citations (Scopus)

Abstract

We present an improved version of parametric time warping, which enables the method to be used in LC-MS measurements in proteomics. The new features include a new similarity measure for comparing warped chromatograms, an insurance against peaks at the extremes of the chromatograms disappearing because of the warping, and the possibility to select and use multiple traces in searching the optimal alignment. Moreover, we present an alignment strategy combining global and individual alignments for aligning LC-MS data that exhibit different shifts within the same sample, at the same retention time. Using an LC-MS data set consisting of E. coil homogenates that were measured in several batches over a period of six months, we show the benefits of the improved algorithm and the merits of the new strategy. The algorithm is publicly available as the R package ptw. (C) 2010 Elsevier B.V. All rights reserved.

Original language	Undefined/Unknown
Pages (from-to)	65-74
Number of pages	10
Journal	Chemometrics & Intelligent Laboratory Systems
Volume	104
Issue number	1
DOIs	https://doi.org/10.1016/j.chemolab.2010.04.008
Publication status	Published - 2010

Research programs

EMC NIHES-01-66-01

Access to Document

10.1016/j.chemolab.2010.04.008

http://hdl.handle.net/1765/27746

Cite this

@article{8269d3847d384f048e5686f06bddc385,

title = "Improved parametric time warping for proteomics",

abstract = "We present an improved version of parametric time warping, which enables the method to be used in LC-MS measurements in proteomics. The new features include a new similarity measure for comparing warped chromatograms, an insurance against peaks at the extremes of the chromatograms disappearing because of the warping, and the possibility to select and use multiple traces in searching the optimal alignment. Moreover, we present an alignment strategy combining global and individual alignments for aligning LC-MS data that exhibit different shifts within the same sample, at the same retention time. Using an LC-MS data set consisting of E. coil homogenates that were measured in several batches over a period of six months, we show the benefits of the improved algorithm and the merits of the new strategy. The algorithm is publicly available as the R package ptw. (C) 2010 Elsevier B.V. All rights reserved.",

author = "TG Bloemberg and J Gerretzen and HJP Wouters and J Gloerich and {van Dael}, M and HJCT Wessels and {van den Heuvel}, LP and Paul Eilers and LMC Buydens and Rik Wehrens",

year = "2010",

doi = "10.1016/j.chemolab.2010.04.008",

language = "Undefined/Unknown",

volume = "104",

pages = "65--74",

journal = "Chemometrics & Intelligent Laboratory Systems",

issn = "0169-7439",

publisher = "Elsevier",

number = "1",

}

TY - JOUR

T1 - Improved parametric time warping for proteomics

AU - Bloemberg, TG

AU - Gerretzen, J

AU - Wouters, HJP

AU - Gloerich, J

AU - van Dael, M

AU - Wessels, HJCT

AU - van den Heuvel, LP

AU - Eilers, Paul

AU - Buydens, LMC

AU - Wehrens, Rik

PY - 2010

Y1 - 2010

N2 - We present an improved version of parametric time warping, which enables the method to be used in LC-MS measurements in proteomics. The new features include a new similarity measure for comparing warped chromatograms, an insurance against peaks at the extremes of the chromatograms disappearing because of the warping, and the possibility to select and use multiple traces in searching the optimal alignment. Moreover, we present an alignment strategy combining global and individual alignments for aligning LC-MS data that exhibit different shifts within the same sample, at the same retention time. Using an LC-MS data set consisting of E. coil homogenates that were measured in several batches over a period of six months, we show the benefits of the improved algorithm and the merits of the new strategy. The algorithm is publicly available as the R package ptw. (C) 2010 Elsevier B.V. All rights reserved.

AB - We present an improved version of parametric time warping, which enables the method to be used in LC-MS measurements in proteomics. The new features include a new similarity measure for comparing warped chromatograms, an insurance against peaks at the extremes of the chromatograms disappearing because of the warping, and the possibility to select and use multiple traces in searching the optimal alignment. Moreover, we present an alignment strategy combining global and individual alignments for aligning LC-MS data that exhibit different shifts within the same sample, at the same retention time. Using an LC-MS data set consisting of E. coil homogenates that were measured in several batches over a period of six months, we show the benefits of the improved algorithm and the merits of the new strategy. The algorithm is publicly available as the R package ptw. (C) 2010 Elsevier B.V. All rights reserved.

U2 - 10.1016/j.chemolab.2010.04.008

DO - 10.1016/j.chemolab.2010.04.008

M3 - Article

SN - 0169-7439

VL - 104

SP - 65

EP - 74

JO - Chemometrics & Intelligent Laboratory Systems

JF - Chemometrics & Intelligent Laboratory Systems

IS - 1

ER -