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An online peak extraction algorithm for ion mobility spectrometry data.

Kopczynski D, Rahmann S - Algorithms Mol Biol (2015)

Bottom Line: Each individual spectrum is processed as it arrives, removing the need to store the measurement before starting the analysis, as is currently the state of the art.Thus the analysis device can be an inexpensive low-power system such as the Raspberry Pi.The key idea is to extract one-dimensional peak models (with four parameters) from each spectrum and then merge these into peak chains and finally two-dimensional peak models.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics for High-Throughput Technologies, Computer Science XI, and Collaborative Research Center SFB 876, TU Dortmund, Dortmund, Germany.

ABSTRACT
Ion mobility (IM) spectrometry (IMS), coupled with multi-capillary columns (MCCs), has been gaining importance for biotechnological and medical applications because of its ability to detect and quantify volatile organic compounds (VOC) at low concentrations in the air or in exhaled breath at ambient pressure and temperature. Ongoing miniaturization of spectrometers creates the need for reliable data analysis on-the-fly in small embedded low-power devices. We present the first fully automated online peak extraction method for MCC/IMS measurements consisting of several thousand individual spectra. Each individual spectrum is processed as it arrives, removing the need to store the measurement before starting the analysis, as is currently the state of the art. Thus the analysis device can be an inexpensive low-power system such as the Raspberry Pi. The key idea is to extract one-dimensional peak models (with four parameters) from each spectrum and then merge these into peak chains and finally two-dimensional peak models. We describe the different algorithmic steps in detail and evaluate the online method against state-of-the-art peak extraction methods.

No MeSH data available.


Related in: MedlinePlus

Visualization of a raw measurement (IMSC) as a heat map; signal color: white (lowest) < blue < purple < red < yellow (highest). The constantly present reactant ion peak (RIP) with mode at 0.48 Vs/cm2 and exemplarily one VOC peak are annotated.
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Fig1: Visualization of a raw measurement (IMSC) as a heat map; signal color: white (lowest) < blue < purple < red < yellow (highest). The constantly present reactant ion peak (RIP) with mode at 0.48 Vs/cm2 and exemplarily one VOC peak are annotated.

Mentions: Let R be the set of (equidistant) retention time points and let T be the set of (equidistant) IRMs where a measurement is made. If D is the corresponding set of drift times (each 1/250000 second for 50 ms, that is 12 500 time points), there exists a constant Ct/d>0 depending on external conditions [12] such that T=Ct/d·D. Then the data is an /R/×/T/ matrix S=(Sr,t) of measured ion intensities, which we call an IM spectrum-chromatogram (IMSC). The matrix can be visualized as a heat map (Figure 1). A row of S is a spectrum, while a column of S is a chromatogram.Figure 1


An online peak extraction algorithm for ion mobility spectrometry data.

Kopczynski D, Rahmann S - Algorithms Mol Biol (2015)

Visualization of a raw measurement (IMSC) as a heat map; signal color: white (lowest) < blue < purple < red < yellow (highest). The constantly present reactant ion peak (RIP) with mode at 0.48 Vs/cm2 and exemplarily one VOC peak are annotated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4495807&req=5

Fig1: Visualization of a raw measurement (IMSC) as a heat map; signal color: white (lowest) < blue < purple < red < yellow (highest). The constantly present reactant ion peak (RIP) with mode at 0.48 Vs/cm2 and exemplarily one VOC peak are annotated.
Mentions: Let R be the set of (equidistant) retention time points and let T be the set of (equidistant) IRMs where a measurement is made. If D is the corresponding set of drift times (each 1/250000 second for 50 ms, that is 12 500 time points), there exists a constant Ct/d>0 depending on external conditions [12] such that T=Ct/d·D. Then the data is an /R/×/T/ matrix S=(Sr,t) of measured ion intensities, which we call an IM spectrum-chromatogram (IMSC). The matrix can be visualized as a heat map (Figure 1). A row of S is a spectrum, while a column of S is a chromatogram.Figure 1

Bottom Line: Each individual spectrum is processed as it arrives, removing the need to store the measurement before starting the analysis, as is currently the state of the art.Thus the analysis device can be an inexpensive low-power system such as the Raspberry Pi.The key idea is to extract one-dimensional peak models (with four parameters) from each spectrum and then merge these into peak chains and finally two-dimensional peak models.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics for High-Throughput Technologies, Computer Science XI, and Collaborative Research Center SFB 876, TU Dortmund, Dortmund, Germany.

ABSTRACT
Ion mobility (IM) spectrometry (IMS), coupled with multi-capillary columns (MCCs), has been gaining importance for biotechnological and medical applications because of its ability to detect and quantify volatile organic compounds (VOC) at low concentrations in the air or in exhaled breath at ambient pressure and temperature. Ongoing miniaturization of spectrometers creates the need for reliable data analysis on-the-fly in small embedded low-power devices. We present the first fully automated online peak extraction method for MCC/IMS measurements consisting of several thousand individual spectra. Each individual spectrum is processed as it arrives, removing the need to store the measurement before starting the analysis, as is currently the state of the art. Thus the analysis device can be an inexpensive low-power system such as the Raspberry Pi. The key idea is to extract one-dimensional peak models (with four parameters) from each spectrum and then merge these into peak chains and finally two-dimensional peak models. We describe the different algorithmic steps in detail and evaluate the online method against state-of-the-art peak extraction methods.

No MeSH data available.


Related in: MedlinePlus