MALDIrppa: quality control and robust analysis for mass spectrometry data

Palarea‐Albaladejo, Javier; McLean, Kevin; Wright, Frank; Smith, David George Emslie

doi:10.1093/bioinformatics/btx628

Cited by 32 publications

(32 citation statements)

References 7 publications

(6 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The .mzXML files of the spectra were then imported into the statistical program R version 3.4.3 in RStudio_version 1.1.423, and submitted to the package MALDIquantforeign_version 0.11.1 . Further analysis used the R packages MALDIquant_version 1.17 and MALDIrppa_version 1.0.1 . Raw spectra were checked for outliers and trimmed to a range of 2 000 to 20 000 Da.…”

Section: Methodsmentioning

confidence: 99%

Concurrent Proteomic Fingerprinting and Molecular Analysis of Cyathostomins

et al. 2019

View full text Add to dashboard Cite

Rapid, cost-effective, efficient, and reliable helminth species identification is of considerable importance to understand host-parasite interactions, clinical disease, and drug resistance. Cyathostomins (Nematoda: Strongylidae) are considered to be the most important equine parasites, yet research on this group is hampered by the large number of 50 morphologically differentiated species, their occurrence in mixed infections with often more than 10 species and the difficulties associated with conventional identification methods. Here, MALDI-TOF MS, previously successfully applied to identify numerous organisms, is evaluated and compared with conventional and molecular genetic approaches. A simple and robust protocol for protein extraction and subsequent DNA isolation allowing molecular confirmation of proteomic findings is developed, showing that MALDI-TOF MS can discriminate adult stages of the two closely related cyathostomin species Cylicostephanus longibursatus and Cylicostephanus minutus. Intraspecific variability of proteomic profiles within morphospecies demonstrated an identification of morphospecies with an accuracy of close to 100%. In contrast, three genospecies within C. minutus and sex-specific profiles within both morphospecies could not be reliably discriminated using MALDI-TOF MS. In conclusion, MALDI-TOF MS complemented by the molecular protocol is a reliable and efficient approach for cyathostomin species identification.

show abstract

Section: Methodsmentioning

confidence: 99%

Concurrent Proteomic Fingerprinting and Molecular Analysis of Cyathostomins

et al. 2019

View full text Add to dashboard Cite

show abstract

“…Noise estimation was carried out with a signal to noise ratio (SNR) of 7. Repeated peak binning was carried out with a tolerance of 0.002 in a strict approach and resulting bins were aligned using R package MALDIrppa (Palarea-Albaladejo, McLean, Wright, & Smith, 2018). For the resulting intensity matrix, missing values were interpolated from the corresponding spectrum.…”

Section: Maldi-tof Msmentioning

confidence: 99%

Recent speciation and hybridization in Icelandic deep-sea isopods: an integrative approach using genomics and proteomics

Paulus

Brix

Siebert

et al. 2021

Preprint

View full text Add to dashboard Cite

The isopod species Haploniscus bicuspis (G.O. Sars, 1877) shows circum-Icelandic distribution in a wide range of environmental conditions and along well-known geographic barriers, such as the Greenland-Iceland-Faroe (GIF) Ridge. We wanted to explore population genetics, phylogeography and cryptic speciation as well as to investigate whether previously described, but unaccepted subspecies have any merit. Using the same set of specimens, we combined mitochondrial COI sequences, thousands of nuclear loci (ddRAD), and proteomic profiles, plus selected morphological characters using Confocal Laser Scanning Microscopy (CLSM). Five divergent genetic lineages were identified by COI and ddRAD, two south and three north of the GIF Ridge. Assignment of populations to the three northern lineages varied and detailed analyses revealed hybridization and gene flow between them, suggesting a single northern species with a complex phylogeographic history. No apparent hybridization was observed among lineages south of the Ridge, inferring the existence of two more species. Differences in proteomic profiles between the three putative species were minimal, implying an ongoing or recent speciation process. Population differentiation was high, even among closely associated populations, and higher in mitochondrial COI than nuclear ddRAD loci. Gene flow is apparently male-biased, leading to hybrid zones and instances of complete exchange of the local nuclear genome through immigrating males. This study did not confirm the existence of subspecies defined by male characters, which probably characterize different male developmental stages present in all species.

show abstract

“…Usually, protein sizes for identification of metazoans are measured within a range from 2000 to 20,000 Da (Laakmann et al 2013; Mazzeo and Siciliano 2016; Rossel and Arbizu 2018). To avoid misidentifications based on poor signal quality, a data processing pipeline to recognize mass spectra of minor quality should be applied (Palarea‐Albaladejo et al 2018).…”

Section: Proteomic Fingerprinting By Maldi‐tof Msmentioning

confidence: 99%

Toward a reliable assessment of potential ecological impacts of deep‐sea polymetallic nodule mining on abyssal infauna

Lins

Zeppilli

Menot

et al. 2021

Limnology & Ocean Methods

View full text Add to dashboard Cite

The increasing demand for metals is pushing forward the progress of deep-sea mining industry. The abyss between the Clarion and Clipperton Fracture Zones (CCFZ), a region holding a higher concentration of minerals than land deposits, is the most targeted area for the exploration of polymetallic nodules worldwide, which may likely disturb the seafloor across large areas and over many years. Effects from nodule extraction cause acute biodiversity loss of organisms inhabiting sediments and polymetallic nodules. Attention to deep-sea ecosystems and their services has to be considered before mining starts but the lack of basic scientific knowledge on the methodologies for the ecological surveys of fauna in the context of deep-sea mining impacts is still scarce. We review the methodology to sample, process and investigate metazoan infauna both inhabiting sediments and nodules dwelling on these polymetallic-nodule areas. We suggest effective procedures for sampling designs, devices and methods involving gear types, sediment processing, morphological and genetic identification including metabarcoding and proteomic fingerprinting, the assessment of biomass, functional traits, fatty acids, and stable isotope studies within the CCFZ based on both first-hand experiences and literature. We recommend multi-and boxcorers for the quantitative assessments of meio-and macrofauna, respectively. The assessment of biodiversity at species level should be focused and/or the combination of morphological with metabarcoding or proteomic fingerprinting techniques. We highlight that biomass, functional traits, and trophic markers may provide critical insights for biodiversity assessments and how statistical modeling facilitates predicting patterns spatially across point-source data and is essential for conservation management.

show abstract

MALDIrppa: quality control and robust analysis for mass spectrometry data

Cited by 32 publications

References 7 publications

Concurrent Proteomic Fingerprinting and Molecular Analysis of Cyathostomins

Concurrent Proteomic Fingerprinting and Molecular Analysis of Cyathostomins

Recent speciation and hybridization in Icelandic deep-sea isopods: an integrative approach using genomics and proteomics

Toward a reliable assessment of potential ecological impacts of deep‐sea polymetallic nodule mining on abyssal infauna

Contact Info

Product

Resources

About