Data from: Effects of sample fixation on specimen identification in biodiversity assemblies based on proteomic data (MALDI-TOF)
Recently, MALDI-TOF mass spectrometry has been used to reliably identify taxonomically difficult harpacticoid copepods from sediment samples. In agreement with former studies, a negative impact of short storage periods was stated. Other studies reported inferior mass spectra quality from samples fix...
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Data Archiving and Networked Services (DANS)
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Online Access: | https://doi.org/10.5061/dryad.1md2jq1 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::7505d381fe2ef768ba9a8c7d30a94fb5 2023-05-15T18:49:42+02:00 Data from: Effects of sample fixation on specimen identification in biodiversity assemblies based on proteomic data (MALDI-TOF) Rossel, Sven Martínez Arbizu, Pedro 2019-04-13 https://doi.org/10.5061/dryad.1md2jq1 undefined unknown Data Archiving and Networked Services (DANS) http://dx.doi.org/10.5061/dryad.1md2jq1 https://dx.doi.org/10.5061/dryad.1md2jq1 lic_creative-commons oai:easy.dans.knaw.nl:easy-dataset:108330 10.5061/dryad.1md2jq1 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:108330 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 Life sciences medicine and health care meiofauna Harpacticus flexus Harpacticoida Ectinosomatidae spec MALDI-TOF MS meiobenthos fixation storage Enhydrosoma propinquum Microarthridion fallax Copepoda Proteome Fingerprint Microarthridion littorale North Sea littoral 53°30.548’N 8°7.445E envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2019 fttriple https://doi.org/10.5061/dryad.1md2jq1 2023-01-22T17:22:31Z Recently, MALDI-TOF mass spectrometry has been used to reliably identify taxonomically difficult harpacticoid copepods from sediment samples. In agreement with former studies, a negative impact of short storage periods was stated. Other studies reported inferior mass spectra quality from samples fixated in varying ethanol concentrations. Therefore, sediment samples from a mudflat sampling site in the North Sea were stored under different temperature conditions to explore a possible storage effect. Samples were fixated with either 70% or 100% ethanol and specimens were measured using MALDI-TOF mass spectrometry after one, two, three, five, seven and 12 weeks. The changes in number of peaks per species and the ability to identify specimens based on mass spectra were analyzed quality measurements. We show that storage temperature had a major impact on data quality, as for some species a loss of up to 50% of mass peaks and an increase of failed measurements to over 70% was observed. However, the effect of different ethanol concentrations on data quality was negligible. Concluding from these results, storage of metazoan samples in general and, particularly, of sediment samples at low temperatures of around -25°C is recommended to receive high-quality mass spectra for specimen identification. Hellinger transformed MALDI-TOF MS intensity matrix of all studied specimensThe dataset contains hellinger transformed MALDI-TOF MS data measured with a Microflex LT/SH System (Bruker Daltonics) with a range from 3,000 to 15,000 m/z from 2,316 harpacticoid copepods from the North Sea (see publication for details). The rows contain the measured species. The first column contains sample names, the second column contains species names, the third column contains measurement weeks, the fourth column contains ethanol concentrations and the fifth column contains storage temperature. The remaining columns contain the 1,220 m/z values as names and the intensities as values.Effects_of_sample_fixation_for_MALDI-TOF.csv Dataset Copepods Harpacticus Unknown |
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Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care meiofauna Harpacticus flexus Harpacticoida Ectinosomatidae spec MALDI-TOF MS meiobenthos fixation storage Enhydrosoma propinquum Microarthridion fallax Copepoda Proteome Fingerprint Microarthridion littorale North Sea littoral 53°30.548’N 8°7.445E envir geo |
spellingShingle |
Life sciences medicine and health care meiofauna Harpacticus flexus Harpacticoida Ectinosomatidae spec MALDI-TOF MS meiobenthos fixation storage Enhydrosoma propinquum Microarthridion fallax Copepoda Proteome Fingerprint Microarthridion littorale North Sea littoral 53°30.548’N 8°7.445E envir geo Rossel, Sven Martínez Arbizu, Pedro Data from: Effects of sample fixation on specimen identification in biodiversity assemblies based on proteomic data (MALDI-TOF) |
topic_facet |
Life sciences medicine and health care meiofauna Harpacticus flexus Harpacticoida Ectinosomatidae spec MALDI-TOF MS meiobenthos fixation storage Enhydrosoma propinquum Microarthridion fallax Copepoda Proteome Fingerprint Microarthridion littorale North Sea littoral 53°30.548’N 8°7.445E envir geo |
description |
Recently, MALDI-TOF mass spectrometry has been used to reliably identify taxonomically difficult harpacticoid copepods from sediment samples. In agreement with former studies, a negative impact of short storage periods was stated. Other studies reported inferior mass spectra quality from samples fixated in varying ethanol concentrations. Therefore, sediment samples from a mudflat sampling site in the North Sea were stored under different temperature conditions to explore a possible storage effect. Samples were fixated with either 70% or 100% ethanol and specimens were measured using MALDI-TOF mass spectrometry after one, two, three, five, seven and 12 weeks. The changes in number of peaks per species and the ability to identify specimens based on mass spectra were analyzed quality measurements. We show that storage temperature had a major impact on data quality, as for some species a loss of up to 50% of mass peaks and an increase of failed measurements to over 70% was observed. However, the effect of different ethanol concentrations on data quality was negligible. Concluding from these results, storage of metazoan samples in general and, particularly, of sediment samples at low temperatures of around -25°C is recommended to receive high-quality mass spectra for specimen identification. Hellinger transformed MALDI-TOF MS intensity matrix of all studied specimensThe dataset contains hellinger transformed MALDI-TOF MS data measured with a Microflex LT/SH System (Bruker Daltonics) with a range from 3,000 to 15,000 m/z from 2,316 harpacticoid copepods from the North Sea (see publication for details). The rows contain the measured species. The first column contains sample names, the second column contains species names, the third column contains measurement weeks, the fourth column contains ethanol concentrations and the fifth column contains storage temperature. The remaining columns contain the 1,220 m/z values as names and the intensities as values.Effects_of_sample_fixation_for_MALDI-TOF.csv |
format |
Dataset |
author |
Rossel, Sven Martínez Arbizu, Pedro |
author_facet |
Rossel, Sven Martínez Arbizu, Pedro |
author_sort |
Rossel, Sven |
title |
Data from: Effects of sample fixation on specimen identification in biodiversity assemblies based on proteomic data (MALDI-TOF) |
title_short |
Data from: Effects of sample fixation on specimen identification in biodiversity assemblies based on proteomic data (MALDI-TOF) |
title_full |
Data from: Effects of sample fixation on specimen identification in biodiversity assemblies based on proteomic data (MALDI-TOF) |
title_fullStr |
Data from: Effects of sample fixation on specimen identification in biodiversity assemblies based on proteomic data (MALDI-TOF) |
title_full_unstemmed |
Data from: Effects of sample fixation on specimen identification in biodiversity assemblies based on proteomic data (MALDI-TOF) |
title_sort |
data from: effects of sample fixation on specimen identification in biodiversity assemblies based on proteomic data (maldi-tof) |
publisher |
Data Archiving and Networked Services (DANS) |
publishDate |
2019 |
url |
https://doi.org/10.5061/dryad.1md2jq1 |
genre |
Copepods Harpacticus |
genre_facet |
Copepods Harpacticus |
op_source |
oai:easy.dans.knaw.nl:easy-dataset:108330 10.5061/dryad.1md2jq1 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:108330 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 |
op_relation |
http://dx.doi.org/10.5061/dryad.1md2jq1 https://dx.doi.org/10.5061/dryad.1md2jq1 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.1md2jq1 |
_version_ |
1766243303317045248 |