Unipept web services for metaproteomics analysis

Mesuere, Bart; Willems, Toon; Jeugt, Felix Van der; Devreese, Bart; Vandamme, Peter; Dawyndt, Peter

doi:10.1093/bioinformatics/btw039

Cited by 49 publications

(39 citation statements)

References 11 publications

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“…In addition to the BLAST homology search, we used Unipept (Mesuere et al. ) to map tryptic peptides to the UniprotKB database and retrieve the least common taxonomic ancestor (most derived shared taxonomic node) associated with each peptide for pooled replicates (Appendix : Fig. S6).…”

Section: Methodsmentioning

confidence: 99%

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem

et al. 2017

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Aquatic ecosystem enrichment can lead to distinct and irreversible changes to undesirable states. Understanding changes in active microbial community function and composition following organic-matter loading in enriched ecosystems can help identify biomarkers of such state changes. In a field experiment, we enriched replicate aquatic ecosystems in the pitchers of the northern pitcher plant, Sarracenia purpurea. Shotgun metaproteomics using a custom metagenomic database identified proteins, molecular pathways, and contributing microbial taxa that differentiated control ecosystems from those that were enriched. The number of microbial taxa contributing to protein expression was comparable between treatments; however, taxonomic evenness was higher in controls. Functionally active bacterial composition differed significantly among treatments and was more divergent in control pitchers than enriched pitchers. Aerobic and facultative anaerobic bacteria contributed most to identified proteins in control and enriched ecosystems, respectively. The molecular pathways and contributing taxa in enriched pitcher ecosystems were similar to those found in larger enriched aquatic ecosystems and are consistent with microbial processes occurring at the base of detrital food webs. Detectable differences between protein profiles of enriched and control ecosystems suggest that a time series of environmental proteomics data may identify protein biomarkers of impending state changes to enriched states.

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Section: Methodsmentioning

confidence: 99%

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem

et al. 2017

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“…Selection was based on the results of preliminary test experiments in which possible transitions were monitored for their ionization and detection efficiency. The specificity of the peptide sequence for a particular protein was verified using the Unipept web server . Protein samples were reduced with dithiothreitol, alkylated with iodoacetamide and digested with sequencing‐grade modified trypsin.…”

Section: Methodsmentioning

confidence: 99%

“…The specificity of the peptide sequence for a particular protein was verified using the Unipept web server. 35 The poor response to BDSF at lower concentrations could be due to active turn-over mechanisms under the conditions used, which requires further investigations. However, the trends we observe agree with previous findings showing that mutation of the BDSF synthase BCAM0581 resulted in decreased ZmpA promoter activity, 25 suggesting that exogenous BSDF could enhance zmpa transcription.…”

Section: Selected Reaction Monitoring (Srm)mentioning

confidence: 99%

Microfluidics‐based liquid chromatography/mass spectrometry multiple reaction monitoring approach for the relative quantification of Burkholderia cenocepacia secreted virulence factors

Depluverez

Daled

Waele

et al. 2018

Rapid Comm Mass Spectrometry

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Burkholderia cenocepacia is an opportunistic pathogen that is commonly isolated from patients with cystic fibrosis (CF). Several virulence factors have been identified, including extracellular enzymes that are secreted by type II and type VI secretion systems. The activity of these secretion systems is modulated by quorum sensing. Apart from the classical acylhomoserine lactone quorum sensing, B. cenocepacia also uses the diffusible signal factor system (DSF) i.e. 2-undecenoic acid derivatives that are recognized by specific receptors resulting in changes in biofilm formation, motility and virulence. However, quantitative information on alterations in the actual production and release of virulence factors upon exposure to DSF is lacking. We here describe an approach implementing microfluidics based chromatography combined with single reaction monitoring to quantify protein virulence factors in the secretome of B. cenocepacia.

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“…Several software tools provide one or more of these features, but have practical and technical limitations that render them unable to facilitate complete analysis pipelines of quantitative proteomics data and scale to the rapidly increasing number of available reference protein sequences 4,5 . With regard to annotating peptides to taxa, Unipept is a commonly used taxonomic annotation tool that can provide access to the entire UniProt sequence repository, provides web-based visualizations and a command line interface, and was demonstrated to annotate peptides orders of magnitude faster than a prior UniProt-based application, Peptide Match 6,7 . However, the Unipept database is unavailable for the end-user to customize, is restricted to a fixed set of assumed experimental parameters such as protease, cannot be used with custom protein databases such as those generated by sequencing, and lacks capability for protein quantitation which limits its utility for analyzing many experimental data sets.…”

Section: Main Textmentioning

confidence: 99%

ProteoClade: a taxonomic toolkit for multi-species and metaproteomic analysis

Mooradian

Post

Naegle

et al. 2019

Preprint

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15We present ProteoClade, a Python toolkit that performs taxa-specific peptide assignment, protein infer-16 ence, and quantitation for multi-species proteomics experiments. ProteoClade scales to hundreds of 17 millions of protein sequences, requires minimal computational resources, and is open source, multi-18 platform, and accessible to non-programmers. We demonstrate its utility for processing quantitative 19 proteomic data derived from patient-derived xenografts and its speed and scalability enable a novel de 20 novo proteomic workflow for complex microbiota samples. 21 22Main Text: 23The goal of metaproteomic and multispecies proteomic studies is to characterize the proteomes of sam-24 ples containing multiple, comingled species, which can provide insight into the complex interactions at 25 the interface between organisms. Proteomic analysis of these samples can quantify thousands of pro-26 teins from hundreds of species in a single mass spectrometry experiment 1 , characterize education of 27 stromal tissue by patient-derived xenografts (PDXs) 2 , and extensively characterize the human oral mi-28 crobiome 3 . 29Metaproteomic and multispecies data analyses depend on the ability to integrate reference protein se-30 quence databases, taxonomic lineages, in silico proteolytic digestion, peptide identification, and quanti-31 tation. These studies universally perform bottom-up analysis, where proteins are digested into peptides 32 with a protease, and therefore require assignment of peptides to proteins based on their taxonomic 33 specificity. Several software tools provide one or more of these features, but have practical and tech-34 nical limitations that render them unable to facilitate complete analysis pipelines of quantitative prote-35 omics data and scale to the rapidly increasing number of available reference protein sequences 4,5 . With 36 regard to annotating peptides to taxa, Unipept is a commonly used taxonomic annotation tool that can 37 provide access to the entire UniProt sequence repository, provides web-based visualizations and a

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Unipept web services for metaproteomics analysis

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 49 publications

References 11 publications

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem

Microfluidics‐based liquid chromatography/mass spectrometry multiple reaction monitoring approach for the relative quantification of Burkholderia cenocepacia secreted virulence factors

ProteoClade: a taxonomic toolkit for multi-species and metaproteomic analysis

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