Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean
Species identification is pivotal in biodiversity assessments and proteomic fingerprinting by MALDI-TOF mass spectrometry has already been shown to reliably identify calanoid copepods to species level. However, MALDI-TOF data may contain more information beyond mere species identification. In this s...
Published in: | Molecular Ecology Resources |
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Main Authors: | , , , , , , , , |
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Wiley
2023
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Online Access: | https://epic.awi.de/id/eprint/58077/ https://epic.awi.de/id/eprint/58077/1/Molecular%20Ecology%20Resources%20-%202022%20-%20Rossel%20-%20Proteomic%20fingerprinting%20enables%20quantitative%20biodiversity%20assessments%20of.pdf https://doi.org/10.1111/1755-0998.13714 https://hdl.handle.net/10013/epic.93f9b960-a295-4e80-8680-3dfd501514b7 |
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ftawi:oai:epic.awi.de:58077 2023-11-12T04:10:13+01:00 Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean Rossel, Sven Kaiser, Patricia Bode‐Dalby, Maya Renz, Jasmin Laakmann, Silke Auel, Holger Hagen, Wilhelm Arbizu, Pedro Martínez Peters, Janna 2023-02 application/pdf https://epic.awi.de/id/eprint/58077/ https://epic.awi.de/id/eprint/58077/1/Molecular%20Ecology%20Resources%20-%202022%20-%20Rossel%20-%20Proteomic%20fingerprinting%20enables%20quantitative%20biodiversity%20assessments%20of.pdf https://doi.org/10.1111/1755-0998.13714 https://hdl.handle.net/10013/epic.93f9b960-a295-4e80-8680-3dfd501514b7 unknown Wiley https://epic.awi.de/id/eprint/58077/1/Molecular%20Ecology%20Resources%20-%202022%20-%20Rossel%20-%20Proteomic%20fingerprinting%20enables%20quantitative%20biodiversity%20assessments%20of.pdf Rossel, S. , Kaiser, P. , Bode‐Dalby, M. , Renz, J. , Laakmann, S. orcid:0000-0003-3273-7907 , Auel, H. , Hagen, W. , Arbizu, P. M. and Peters, J. (2023) Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean , Molecular Ecology Resources, 23 (2), pp. 382-395 . doi:10.1111/1755-0998.13714 <https://doi.org/10.1111/1755-0998.13714> , hdl:10013/epic.93f9b960-a295-4e80-8680-3dfd501514b7 EPIC3Molecular Ecology Resources, Wiley, 23(2), pp. 382-395, ISSN: 1755-098X Article peerRev 2023 ftawi https://doi.org/10.1111/1755-0998.13714 2023-10-30T00:23:13Z Species identification is pivotal in biodiversity assessments and proteomic fingerprinting by MALDI-TOF mass spectrometry has already been shown to reliably identify calanoid copepods to species level. However, MALDI-TOF data may contain more information beyond mere species identification. In this study, we investigated different ontogenetic stages (copepodids C1–C6 females) of three co-occurring Calanus species from the Arctic Fram Strait, which cannot be identified to species level based on morphological characters alone. Differentiation of the three species based on mass spectrometry data was without any error. In addition, a clear stage-specific signal was detected in all species, supported by clustering approaches as well as machine learning using Random Forest. More complex mass spectra in later ontogenetic stages as well as relative intensities of certain mass peaks were found as the main drivers of stage distinction in these species. Through a dilution series, we were able to show that this did not result from the higher amount of biomass that was used in tissue processing of the larger stages. Finally, the data were tested in a simulation for application in a real biodiversity assessment by using Random Forest for stage classification of specimens absent from the training data. This resulted in a successful stage-identification rate of almost 90%, making proteomic fingerprinting a promising tool to investigate polewards shifts of Atlantic Calanus species and, in general, to assess stage compositions in biodiversity assessments of Calanoida, which can be notoriously difficult using conventional identification methods. Article in Journal/Newspaper Arctic Arctic Arctic Ocean Fram Strait Copepods Alfred Wegener Institute for Polar- and Marine Research (AWI): ePIC (electronic Publication Information Center) Molecular Ecology Resources 23 2 382 395 |
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Open Polar |
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Alfred Wegener Institute for Polar- and Marine Research (AWI): ePIC (electronic Publication Information Center) |
op_collection_id |
ftawi |
language |
unknown |
description |
Species identification is pivotal in biodiversity assessments and proteomic fingerprinting by MALDI-TOF mass spectrometry has already been shown to reliably identify calanoid copepods to species level. However, MALDI-TOF data may contain more information beyond mere species identification. In this study, we investigated different ontogenetic stages (copepodids C1–C6 females) of three co-occurring Calanus species from the Arctic Fram Strait, which cannot be identified to species level based on morphological characters alone. Differentiation of the three species based on mass spectrometry data was without any error. In addition, a clear stage-specific signal was detected in all species, supported by clustering approaches as well as machine learning using Random Forest. More complex mass spectra in later ontogenetic stages as well as relative intensities of certain mass peaks were found as the main drivers of stage distinction in these species. Through a dilution series, we were able to show that this did not result from the higher amount of biomass that was used in tissue processing of the larger stages. Finally, the data were tested in a simulation for application in a real biodiversity assessment by using Random Forest for stage classification of specimens absent from the training data. This resulted in a successful stage-identification rate of almost 90%, making proteomic fingerprinting a promising tool to investigate polewards shifts of Atlantic Calanus species and, in general, to assess stage compositions in biodiversity assessments of Calanoida, which can be notoriously difficult using conventional identification methods. |
format |
Article in Journal/Newspaper |
author |
Rossel, Sven Kaiser, Patricia Bode‐Dalby, Maya Renz, Jasmin Laakmann, Silke Auel, Holger Hagen, Wilhelm Arbizu, Pedro Martínez Peters, Janna |
spellingShingle |
Rossel, Sven Kaiser, Patricia Bode‐Dalby, Maya Renz, Jasmin Laakmann, Silke Auel, Holger Hagen, Wilhelm Arbizu, Pedro Martínez Peters, Janna Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean |
author_facet |
Rossel, Sven Kaiser, Patricia Bode‐Dalby, Maya Renz, Jasmin Laakmann, Silke Auel, Holger Hagen, Wilhelm Arbizu, Pedro Martínez Peters, Janna |
author_sort |
Rossel, Sven |
title |
Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean |
title_short |
Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean |
title_full |
Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean |
title_fullStr |
Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean |
title_full_unstemmed |
Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean |
title_sort |
proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in calanus congeners (copepoda, crustacea) from the arctic ocean |
publisher |
Wiley |
publishDate |
2023 |
url |
https://epic.awi.de/id/eprint/58077/ https://epic.awi.de/id/eprint/58077/1/Molecular%20Ecology%20Resources%20-%202022%20-%20Rossel%20-%20Proteomic%20fingerprinting%20enables%20quantitative%20biodiversity%20assessments%20of.pdf https://doi.org/10.1111/1755-0998.13714 https://hdl.handle.net/10013/epic.93f9b960-a295-4e80-8680-3dfd501514b7 |
genre |
Arctic Arctic Arctic Ocean Fram Strait Copepods |
genre_facet |
Arctic Arctic Arctic Ocean Fram Strait Copepods |
op_source |
EPIC3Molecular Ecology Resources, Wiley, 23(2), pp. 382-395, ISSN: 1755-098X |
op_relation |
https://epic.awi.de/id/eprint/58077/1/Molecular%20Ecology%20Resources%20-%202022%20-%20Rossel%20-%20Proteomic%20fingerprinting%20enables%20quantitative%20biodiversity%20assessments%20of.pdf Rossel, S. , Kaiser, P. , Bode‐Dalby, M. , Renz, J. , Laakmann, S. orcid:0000-0003-3273-7907 , Auel, H. , Hagen, W. , Arbizu, P. M. and Peters, J. (2023) Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean , Molecular Ecology Resources, 23 (2), pp. 382-395 . doi:10.1111/1755-0998.13714 <https://doi.org/10.1111/1755-0998.13714> , hdl:10013/epic.93f9b960-a295-4e80-8680-3dfd501514b7 |
op_doi |
https://doi.org/10.1111/1755-0998.13714 |
container_title |
Molecular Ecology Resources |
container_volume |
23 |
container_issue |
2 |
container_start_page |
382 |
op_container_end_page |
395 |
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1782329797371756544 |