{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025681/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025681/WT-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025681/WT-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025681/Mut-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025681/Mut-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025681/WT-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025681/Mut-2.raw"],"Mzid":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025681/S.oneidensis_Results.mzid.gz"],"Mgf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025681/WT-1.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025681/Mut-2.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025681/Mut-1.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025681/WT-2.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025681/Mut-3.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025681/WT-3.mgf"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["virginie.brun@cea.fr"],"submitter":["Yohann Couté"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"software":["Xcalibur","Mascot","Proline"],"submitter_keywords":["Riboflavin production","Nanolc-ms/ms","Biofilm formation","Shewanella oneidensis","Putrescin decarboxylase spec"],"full_dataset_link":["http://www.ebi.ac.uk/pride/archive/projects/PXD025681"],"sample_protocol":["Proteomic analyses were conducted with cells that were inoculated in anoxic M4 minimal media with 70 mM lactate as electron donor and 100 mM fumarate as electron acceptor. The starting OD600 was 0.2. After 5 h of growth, cells were harvested by centrifugation (7 min, 6000 g, 4°C). The supernatant was discarded, and pellets were resuspended in TRIS buffer (pH 6.8). Cells were lysed by two passages through a French Press. Cell lysates were mixed with Laemmli buffer and then stacked in a single band in the top of a sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gel (4%–12% NuPAGE gel, Invitrogen, Illkirch-Grafenstaden/France). After staining with R-250 Coomassie Blue (Biorad, Schiltigheim/France), proteins were digested in gel using modified trypsin (sequencing grade, Promega, Charbonnières les Bains/France). Resulting peptides were analyzed by online nano-liquid chromatography coupled to tandem mass spectrometry (MS) (Ultimate 3000 RSLCnano and Q-Exactive HF, Thermo Scientific, Illkirch-Grafenstaden/France). For this purpose, peptides were sampled on a 300 μm × 5 mm PepMap C18 precolumn (Thermo Scientific, Illkirch- Grafenstaden/France) and separated on a 75 μm x 250 mm C18 column (Reprosil-Pur 120 C18-AQ, 1.9 μm, Dr. Maisch, Ammerbuch-Entringen) using a 180-min gradient."],"repository":["Pride"],"quantification_method":["Not available"],"modification":["iodoacetamide derivatized residue","monohydroxylated residue","acetylated residue"],"data_protocol":["The MS and MS/MS data were collected by Xcalibur (Thermo Scientific, Illkirch-Grafenstaden/France). Peptides and proteins were identified by Mascot (Matrix Science, London/United Kingdom) through concomitant searches against the Uniprot database (S. oneidensis MR-1 taxonomy), a homemade classical contaminant database, and the corresponding reversed databases. Trypsin/P was chosen as the enzyme, and two missed cleavages were allowed. Precursor and fragment mass error tolerances were set at respectively at 10 and 25 mmu. Peptide modifications allowed during the search were carbamidomethyl (C, fixed), Acetyl (Protein N-term, variable) and oxidation (M, variable). The Proline software was used to filter the results with conservation of rank 1 peptides, peptide score ≥ 25, peptide length ≥ 7 amino acids, FDR of peptide-spectrum-match identifications < 1% as calculated on peptide spectrum-match scores by employing the reverse database strategy, and a minimum of 1 specific peptide per identified protein group. Proline was then used to perform a compilation, grouping and MS1 quantification of the validated protein groups."],"omics_type":["Proteomics"],"labhead":["Virginie Brun"],"instrument_platform":["Q Exactive HF"],"labhead_affiliation":["EDyP"],"submission_type":["COMPLETE"],"species":["Shewanella Oneidensis (strain Mr-1)"],"submitter_mail":["yohann.coute@cea.fr"],"publication":["34082787 Edel M, Sturm G, Sturm-Richter K, Wagner M, Ducassou JN, Couté Y, Horn H, Gescher J. Extracellular riboflavin induces anaerobic biofilm formation in Shewanella oneidensis. Biotechnol Biofuels. 2021 14(1):130 10.1186/s13068-021-01981-3"],"submitter_affiliation":["EDyP"],"submitter_country":["France"],"doi":["10.6019/PXD025681"],"pubmed_abstract":["