Watershed Segmentation for Peak Picking in Mass Spectrometry
Data

D 2020

Watershed Segmentation for Peak Picking in Mass Spectrometry Data

BARTOŇ, Vojtěch, Markéta NYKRÝNOVÁ a Helena ŠKUTKOVÁ

Základní údaje

Originální název

Watershed Segmentation for Peak Picking in Mass Spectrometry Data

Autoři

BARTOŇ, Vojtěch (203 Česká republika, garant, domácí), Markéta NYKRÝNOVÁ (203 Česká republika) a Helena ŠKUTKOVÁ (203 Česká republika)

Vydání

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

Nakladatel

Springer

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

elektronická verze "online"

Odkazy

URL

Impakt faktor

Impact factor: 0.402 v roce 2005

Kód RIV

RIV/00216224:14310/20:00129898

Organizační jednotka

Přírodovědecká fakulta

ISBN

978-3-030-45384-8

ISSN

DOI

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

UT WoS

000892623400044

Klíčová slova anglicky

Mass spectrometry; Peak picking; Image segmentation

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 4. 4. 2024 15:49, Mgr. Marie Novosadová Šípková, DiS.

Anotace

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.

Návaznosti

LM2015085, projekt VaV

Název: CERIT Scientific Cloud (Akronym: CERIT-SC)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CERIT Scientific Cloud

LM2018121, projekt VaV

Název: Výzkumná infrastruktura RECETOX (Akronym: RECETOX RI)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, RECETOX RI

90042, velká výzkumná infrastruktura

Název: CESNET II

Citovat

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

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