Mayfly and fish species identification and sex determination in bleak (Alburnus alburnus) by MALDI-TOF mass spectrometry

A universal tool for marine metazoan species identification: towards best practices in proteomic fingerprinting

Proteomic fingerprinting using MALDI-TOF mass spectrometry is a well-established tool for identifying microorganisms and has shown promising results for identification of animal species, particularly disease vectors and marine organisms. And thus can be a vital tool for biodiversity assessments in ecological studies. However, few studies have tested species identification across different orders and classes. In this study, we collected data from 1246 specimens and 198 species to test species identification in a diverse dataset. We also evaluated different specimen preparation and data processing approaches for machine learning and developed a workflow to optimize classification using random forest. Our results showed high success rates of over 90%, but we also found that the size of the reference library affects classification error. Additionally, we demonstrated the ability of the method to differentiate marine cryptic-species complexes and to distinguish sexes within species.

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 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.

Identification of ticks from an old collection by MALDI-TOF MS

Objective of this study is to find the optimal conditions for preparing the samples, resulting in quality, reproducible and specific MS spectra of the ticks, with a shelf life in 70% ethanol of more than ten years. Amblyomma (Am.) variegatum species which had been stored in alcohol for more than twenty years and for which numerous specimens were available were used to compare the performance of four protocols tested. Spectra of insufficient quality were obtained from Am. variegatum legs preserved in alcohol for long periods with the reference protocol, named DO that we had set up years ago. The same observation was made on the spectra from Am. variegatum legs from dry (evaporated alcohol, DO-mod protocol). With new protocols named ReDO and PReDO the spectra were of good quality with high intensities (> 3000 a.u.). Blind testing showed that 94%, and 93% of the spectra were correctly identified with relevant log score values (LSVs ≥1.8), respectively for ReDO and PReDO protocols. All soft ticks treated in this study by PReDO protocol exhibited low intensity spectra with background noise. This study revealed that MALDI-TOF MS is able to identify hard ticks stored during decades in alcohol or dry (evaporated alcohol). SIGNIFICANCE OF THE STUDY: The correct identification of ticks, including vectors responsible for the transmission of infectious diseases in humans and animals is essential for their control. MALDI-TOF MS, a proteomic tool that has emerged in recent years, has become an innovative, accurate and alternative tool for the identification of arthropods, including ticks. However, previous studies reported that preservation of arthropods in alcohol modified the MS spectra obtained from specimens of the same species freshly collected or frozenly stored. In this study, a standard protocol was established for the identification of tick collections which had been stored for more than ten years in alcohol. Four different protocols were assessed. The analysis of the results showed that among the four protocols tested, two protocols named ReDO (Rehydration and incubation of the legs in 40 μl of HPLC water for 12 h in a dry bath at 37°) and PreDO (Drying of the legs for 12 h in a dry bath at 37 °C followed by rehydration and incubation in 40 μl of HPLC water for 12 h.) seem to be more appropriate for the MALDI-TOF MS identification of ticks from old collections preserved in alcohol or dry. This study is promising for the future, as it will make it possible to create a MALDI-TOF MS database from a wide range of ticks which have been stored for a long time in alcohol or which are dry stored in laboratories and museums around the world.

Rapid species level identification of fish eggs by proteome fingerprinting using MALDI-TOF MS

Quantifying spawning biomass of commercially relevant fish species is important to generate fishing quotas. This will mostly rely on the annual or daily production of fish eggs. However, these have to be identified precisely to species level to obtain a reliable estimate of offspring production of the different species. Because morphological identification can be very difficult, recent developments are heading towards application of molecular tools. Methods such as COI barcoding have long handling times and cause high costs for single specimen identifications. In order to test MALDI-TOF MS, a rapid and cost-effective alternative for species identification, we identified fish eggs using COI barcoding and used the same specimens to set up a MALDI-TOF MS reference library. This library, constructed from two different MALDI-TOF MS instruments, was then used to identify unknown eggs from a different sampling occasion. By using a line of evidence from hierarchical clustering and different supervised identification approaches we obtained concordant species identifications for 97.5% of the unknown fish eggs, proving MALDI-TOF MS a good tool for rapid species level identification of fish eggs. At the same time we point out the necessity of adjusting identification scores of supervised methods for identification to optimize identification success. SIGNIFICANCE: Fish products are commercially highly important and many societies rely on them as a major food resource. Over many decades stocks of various relevant fish species have been reduced due to unregulated overfishing. Nowadays, to avoid overfishing and threatening of important fish species, fish stocks are regularly monitored. One component of this monitoring is the monitoring of spawning stock sizes. Whereas this is highly dependent on correct species identification of fish eggs, morphological identification is difficult because of lack of morphological features.

Testing the Applicability of MALDI-TOF MS as an Alternative Stock Identification Method in a Cryptic Species Complex

Knowledge of intraspecific variability of a certain species is essential for their long-term survival and for the development of conservation plans. Nowadays, molecular/genetic methods are the most frequently used for this purpose. Although, the Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) technique has become a promising alternative tool to specify intraspecific variability, there is a lack of information about the limitations of this method, and some methodological issues need to be resolved. Towards this goal, we tested the sensitivity of this method on an intraspecific level, using genetically identified individuals of a cryptic fish species complex collected from five distinct populations. Additionally, some methodologic issues, such as the effect of (1) delayed sample preparation, (2) clove oil anaesthetization, and (3) different tissue types (muscle, and brain) were investigated using the MS analysis results. Our results show that the delayed sample preparation has a fundamental effect on the result of MS analysis, while at the same time the clove oil did not affect the results considerably. Both the brain and muscle samples were usable for cryptic species identification, but in our opinion this method has limited applicability for population-level segregation. The application of MALDI-TOF MS to the exploitable toolkit of phylogenetic and taxonomic researches could be used to broaden conclusions.

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

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.

Detection methods for Pseudomonas aeruginosa: history and future perspective

The current review summarized and analyzed the development of detection techniques forPseudomonas aeruginosaover the past 50 years.