Watershed Segmentation for Peak Picking in Mass Spectrometry
Data

D 2020

Watershed Segmentation for Peak Picking in Mass Spectrometry Data

BARTOŇ, Vojtěch, Markéta NYKRÝNOVÁ and Helena ŠKUTKOVÁ

Basic information

Original name

Watershed Segmentation for Peak Picking in Mass Spectrometry Data

Authors

BARTOŇ, Vojtěch (203 Czech Republic, guarantor, belonging to the institution), Markéta NYKRÝNOVÁ (203 Czech Republic) and Helena ŠKUTKOVÁ (203 Czech Republic)

Edition

Berlin, International Work-Conference on Bioinformatics and Biomedical Engineering, p. 494-502, 9 pp. 2020

Publisher

Springer

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Germany

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

electronic version available online

References:

URL

Impact factor

Impact factor: 0.402 in 2005

RIV identification code

RIV/00216224:14310/20:00129898

Organization unit

Faculty of Science

ISBN

978-3-030-45384-8

ISSN

DOI

http://dx.doi.org/10.1007/978-3-030-45385-5_44

UT WoS

000892623400044

Keywords in English

Mass spectrometry; Peak picking; Image segmentation

Abstract

V originále

Mass spectrometry with gas chromatography is one of the emerging high-resolution instruments. This technology can be used to discover the composition of the chemical compounds. It is used for targeted detection or for untargeted screening. As such, this technology is providing a large volume of measurements. These data are also in high precision. There are emerging need to efficiently process these data and be able to identify and extract all possible information. There are numerous tools to do that, using common steps. One of the steps is peak picking, usually carried by signal processing methods. We are proposing a two-dimensional approach to identify the peaks and extract their features for further analysis. This method can be easily adaptable to fit the current pipelines and to perform the computation efficiently. We are proposing a method to preprocess the data onto a grid of required precision. After that, we are applying an image processing method watershed, to extract the region of interest and the peaks.

Links

LM2015085, research and development project

Name: CERIT Scientific Cloud (Acronym: CERIT-SC)

Investor: Ministry of Education, Youth and Sports of the CR, CERIT Scientific Cloud

LM2018121, research and development project

Name: Výzkumná infrastruktura RECETOX (Acronym: RECETOX RI)

Investor: Ministry of Education, Youth and Sports of the CR, RECETOX RI

90042, large research infrastructures

Name: CESNET II

Citovat

BARTOŇ, Vojtěch, Markéta NYKRÝNOVÁ and Helena ŠKUTKOVÁ. Watershed Segmentation for Peak Picking in Mass Spectrometry Data. Online. In International Work-Conference on Bioinformatics and Biomedical Engineering. Berlin: Springer, 2020, p. 494-502. ISBN 978-3-030-45384-8. Available from: https://dx.doi.org/10.1007/978-3-030-45385-5_44.

@inproceedings{1709216,
   author = {Bartoň, Vojtěch and Nykrýnová, Markéta and Škutková, Helena},
   address = {Berlin},
   booktitle = {International Work-Conference on Bioinformatics and Biomedical Engineering},
   doi = {http://dx.doi.org/10.1007/978-3-030-45385-5_44},
   keywords = {Mass spectrometry; Peak picking; Image segmentation},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Berlin},
   isbn = {978-3-030-45384-8},
   pages = {494-502},
   publisher = {Springer},
   title = {Watershed Segmentation for Peak Picking in Mass Spectrometry Data},
   url = {https://link.springer.com/chapter/10.1007/978-3-030-45385-5_44},
   year = {2020}
}

TY  - JOUR
ID  - 1709216
AU  - Bartoň, Vojtěch - Nykrýnová, Markéta - Škutková, Helena
PY  - 2020
TI  - Watershed Segmentation for Peak Picking in Mass Spectrometry Data
PB  - Springer
CY  - Berlin
SN  - 9783030453848
KW  - Mass spectrometry
KW  - Peak picking
KW  - Image segmentation
UR  - https://link.springer.com/chapter/10.1007/978-3-030-45385-5_44
N2  - Mass spectrometry with gas chromatography is one of the emerging high-resolution instruments. This technology can be used to discover the composition of the chemical compounds. It is used for targeted detection or for untargeted screening. As such, this technology is providing a large volume of measurements. These data are also in high precision. There are emerging need to efficiently process these data and be able to identify and extract all possible information. There are numerous tools to do that, using common steps. One of the steps is peak picking, usually carried by signal processing methods. We are proposing a two-dimensional approach to identify the peaks and extract their features for further analysis. This method can be easily adaptable to fit the current pipelines and to perform the computation efficiently. We are proposing a method to preprocess the data onto a grid of required precision. After that, we are applying an image processing method watershed, to extract the region of interest and the peaks.
ER  -

BARTOŇ, Vojtěch, Markéta NYKRÝNOVÁ and Helena ŠKUTKOVÁ. Watershed Segmentation for Peak Picking in Mass Spectrometry Data. Online. In \textit{International Work-Conference on Bioinformatics and Biomedical Engineering}. Berlin: Springer, 2020, p.~494-502. ISBN~978-3-030-45384-8. Available from: https://dx.doi.org/10.1007/978-3-030-45385-5\_{}44.

Detailed Information on Publication Record