Effects of Sample Fixation on Specimen Identification in Biodiversity Assemblies Based on Proteomic Data (MALDI-TOF)

Rossel, Sven; Arbizu, Pedro Martínez

doi:10.3389/fmars.2018.00149

Cited by 21 publications

(39 citation statements)

References 54 publications

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“…30 for calanoid copepods. Successful identification of smaller harpacticoid copepods was already shown by Rossel and Martínez Arbizu 31,32 . Amongst others, the authors emphasized the importance of sediment sample storage at low temperatures for MALDI-TOF MS applications 32 .…”

Section: Introductionmentioning

confidence: 74%

Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding

Rossel

Arbizu

2019

Sci Rep

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The North Sea is one of the most extensively studied marine regions of the world. Hence, large amounts of molecular data for species identification are available in public repositories, and expectations to find numerous new species in this well-known region are rather low. However, molecular reference data for harpacticoid copepods from this area in particular but also for this group in general is scarce. By assessing COI barcodes and MALDI-TOF mass spectra for this group of small crustaceans, it was discovered that there is a huge unknown diversity in this area. In total, COI sequences for 548 specimens from 115 species of harpacticoid copepods are presented. Over 19% of these were new to science and ten MOTUs were found to be part of cryptic species complexes. MALDI-TOF mass spectra were assessed for 622 specimens from 75 species. Because results were in concordance with species delimitation by COI barcoding and also enabled recognition of possible cryptic species, the discriminative power of this technique for biodiversity assessments is highlighted. Findings imply, species diversity in this group may be largely underestimated and total species number can be expected to be much higher than previously assumed.

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Section: Introductionmentioning

confidence: 74%

Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding

Rossel

Arbizu

2019

Sci Rep

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“…Simultaneous use of individuals for barcoding and analysis in MALDI-TOF MS was shown several times (e.g., Laakmann et al, 2013;Bode et al, 2017;Rossel and Martínez Arbizu, 2018b;Rossel and Martínez Arbizu, 2019) even for small animals such as copepods, implying a possible combination of MALDI-TOF MS and DNA barcoding for biodiversity assessments and monitoring. Voucher specimens can be analyzed by MALDI-TOF MS and sequenced simultaneously to support identifications based on mass spectra by DNA without causing high costs by barcoding of all assessed specimens.…”

Section: Maldi-tof Ms Vs Barcoding Vs Metabarcodingmentioning

confidence: 99%

Comparison of Rapid Biodiversity Assessment of Meiobenthos Using MALDI-TOF MS and Metabarcoding

2019

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Nowadays, most biodiversity assessments involving meiofauna are mainly carried out using very time-consuming, specimen-wise morphological identifications, which demands comprehensive taxonomic knowledge. Animals have to be examined for minor differences of setae compositions, mouthpart morphology or number of segments for various extremities. DNA-based methods such as metabarcoding as well as recently emerged rapid analyses using MALDI-TOF mass spectrometry to identify specimens based on a proteome fingerprint could vastly accelerate the process of specimen identification in biodiversity assessments. However, these techniques depend on reference libraries to connect collected data to morphologically described species. In this study the success rate of both approaches have been tested based on reference libraries constructed using part of the samples from a new study area to identify unknown samples. Using MALDI-TOF MS we found, that species which do not exist in an incomplete mass spectra reference library only have minor impact on the results, when employing a post hoc test for Random Forest classifications. This test reveals specimens that demand morphological re-examination for the final species assignment. Metabarcoding however strongly demands a rich reference library to provide correct MOTU assessments in congruence with morphological determination. Nevertheless, with a complete library and a suitable data transformation [herein log(x + 1)], the number of reads per MOTU reflects relative species abundances in metabarcoding inference. The results of this study facilitate specimen identification by using MALDI-TOF MS, which is incomparably cheap for specimen-by-specimen identification, but when it comes to sample-wise analyses, metabarcoding outperforms other techniques by far.

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“…When applying the workflow presented here, attention has to be paid to data origin and quality. For instance, joining data from different studies may cause problems as various factors such as storage and fixation were shown to influence mass spectra quality (Yssouf et al ; Rossel and Martínez Arbizu ). This may affect the species‐specific fingerprint in such a way that single species could be recognized as different species due to mass spectra alteration.…”

Section: Discussionmentioning

confidence: 99%

“…MALDI‐TOF MS data from published mass spectra (Rossel and Martínez Arbizu , c , , b ; Supporting Information Table S1) on harpacticoid copepods were pooled and screened for species with at least 10 specimens. Only specimens reported to be obtained from appropriately stored samples were included and combined into the data set used for this study.…”

Section: Methodsmentioning

confidence: 99%

“…Our workflow for unsupervised biodiversity estimation demands reanalyzing the data set as many times as there are specimens in the data set. Computational effort can be very high because data sets may contain several hundred m/z values (Rossel and Martínez Arbizu , ). Therefore, dimensionality reduction is an important step to reduce computational resources needed.…”

Section: Methodsmentioning

confidence: 99%

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Unsupervised biodiversity estimation using proteomic fingerprints fromMALDI‐TOF MSdata

Rossel

Arbizu

2020

Limnology & Ocean Methods

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Species identification using matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) data strongly relies on reference libraries to differentiate species. Because comprehensive reference libraries, especially for metazoans, are rare, we explored the accuracy of unsupervised diversity estimations of communities using MALDI-TOF MS data in the absence of reference libraries to provide a method for future application in ecological research. To discover the best analysis strategy providing high congruence with true community structures, we carried out a simulation with more than 30,000 analyses using different combinations of data transformations, dimensionality reductions, and cluster algorithms. Species profile, Hellinger, and presence/absence transformations were applied to raw data and dimensions were reduced using principal component analysis (PCA), t-distributed stochastic neighbor embedding, and uniform manifold approximation and projection. To estimate biodiversity, data were clustered making use of partitioning around medoids, modelbased clustering, and K-means clustering. The analyses were carried out on published mass spectrometry data of harpacticoid copepods. Most successful combinations (Hellinger transformation + PCA or raw data + partitioning around medoids) returned good values even for difficult species distributions containing numerous singleton species. Nevertheless, errors occurred most frequently because of such singleton taxa. Hence, replicative sampling in wide sampling areas for analysis is emphasized to increase the minimum number of specimens per species, thus reducing putative sources of errors. Our results demonstrate that MALDI-TOF MS data can be used to accurately estimate the biodiversity of unknown communities using unsupervised learning methods. The provided approach allows the biodiversity comparison of sampled regions for which no reference libraries are available. Hence, especially data on groups which demand a time-consuming identification or are highly abundant can be analyzed within short working time, accelerating ecological studies.

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Effects of Sample Fixation on Specimen Identification in Biodiversity Assemblies Based on Proteomic Data (MALDI-TOF)

Cited by 21 publications

References 54 publications

Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding

Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding

Comparison of Rapid Biodiversity Assessment of Meiobenthos Using MALDI-TOF MS and Metabarcoding

Unsupervised biodiversity estimation using proteomic fingerprints fromMALDI‐TOF MSdata

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