Dataset Information

Paenibacillus larvae exoproteins of ERIC I-IV genotypes

ABSTRACT: The following strains of Paenibacillus larvae classified as ERIC I-IV genotypes (pl1-pl4) were used in the study: ERIC I - DSM-7030; ERIC II - DSM-25430; ERIC III - LMG-16252; and ERIC IV - DSM-3615. The 7 biological replicates (a-g) of the exoprotein fractions prepared from each ERIC genotype were used in the nanoLC-MS/MS analysis. All 28 samples were consecutively analyzed using an OrbitrapTM FusionTM Tribrid q-OT-IT mass spectrometer. To improve the protein identification and easy exclude contaminants from the medium, we considered the proteins that could originate from the yeast extract and Mueller-Hinton broth (contains beef fusion and casein peptone-acidic hydrolysate) in analyzing the MS data. Thus, we included the sequences related to Saccharomyces cerevisiae and Bos taurus, respectively, to the list of contaminants in MaxQuant. The contaminants.fasta file is provided. Futhermore, we provide the database (uniprot-paenibacillus+larvae.fasta) used for the identification of P. larvae proteins created of different strains of P. larvae. The sequences were downloaded of UniProt on 12.03.2019. Finally, the compressed (zipped) folder "combined" is provided. The data were analyzed in MaxQuant v1.6.3.4.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Paenibacillus Larvae (ncbitaxon:1464)

SUBMITTER: Tomas Erban

PROVIDER: MSV000083636 | MassIVE | Wed Mar 27 15:52:00 GMT 2019

SECONDARY ACCESSION(S): PXD013272

REPOSITORIES: MassIVE

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Publications

Comprehensive proteomic analysis of exoproteins expressed by ERIC I, II, III and IV Paenibacillus larvae genotypes reveals a wide range of virulence factors.

Erban Tomas T Zitek Justyna J Bodrinova Miroslava M Talacko Pavel P Bartos Milan M Hrabak Jaroslav J

Virulence 20191201 1

American foulbrood is a quarantine disease of the honeybee Apis mellifera L. in many countries and contributes greatly to colony losses. We performed a label-free proteomics study of exoprotein fractions produced in vitro by Paenibacillus larvae reference strains of the ERIC I-IV genotypes. A quantitative comparison was performed of previous studied protein-based virulence factors and many newly identified putative virulence factors. Among the multiple proteases identified, key virulence factors ...[more]

PMID: 30957692

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Project description:Proteomic sample preparation typically involves multi-step workflows that can potentially perturb the biological system under analysis. These datasets were used to demonstrate that the entire processing pipeline, from cell lysis through elution of purified peptides, can be performed in a single, enclosed volume. This in-StageTip sample preparation method largely eliminates contamination or losses and is extremely robust and scalable. Peptides can be eluted in several fractions or in one step for single-run proteomics. In one day of gradient time we obtained the largest proteomes for budding and fission yeast to date. Applying the in-StageTip method to quadruplicate measurements of a human cell line yielded copy number estimates for more than 9000 human proteins. Data Analysis: MS raw files were analyzed by MaxQuant software (version 1.3.10.12) and peak lists were searched either against the human Uniprot FASTA database version 2/25/2012 (81213 entries), against the S. cerevisiae Uniprot FASTA database version 2/25/2012 (6649 entries) or the SGD based S. cerevisiae Fasta database orf_trans.20100105 (5904 entries), or against the S. pombe Uniprot FASTA database version 4/2/2013 (5096 entries) or pompep FASTA database version 4/2/2013 (5031 entries) and a common contaminants database (247 entries) by Andromeda search engine with cysteine carbamidomethylation as a fixed modification and N-terminal acetylation and methionine oxidation as variable modifications. False discovery rate (FDR) was set to 0.01 for proteins and peptides (minimum length of 7 amino acids) and was determined by searching a reverse database. Enzyme specificity was set as C-terminal to Arg and Lys, and a maximum of 2 miscleavages allowed. Peptide identification was performed with an allowed initial precursor mass deviation up to 7 ppm and an allowed fragment mass deviation 20 ppm. Quantification of SILAC pairs was carried out by MaxQuant with standard settings and without the re-quantification option.

Dataset Information

Paenibacillus larvae exoproteins of ERIC I-IV genotypes

Publications

Comprehensive proteomic analysis of exoproteins expressed by ERIC I, II, III and IV Paenibacillus larvae genotypes reveals a wide range of virulence factors.

Similar Datasets

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