{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_3hr_MOI_20_infected_B3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_3hr_Uninfected_B3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_24hr_Uninfected_B1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_3hr_MOI_20_infected_B1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_24hr_MOI_20_infected_B1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_24hr_Uninfected_B3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_3hr_Uninfected_B1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_24hr_MOI_20_infected_B3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_3hr_MOI_20_infected_B4.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_3hr_MOI_20_infected_B2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_3hr_Uninfected_B4.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_3hr_Uninfected_B2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_24hr_Uninfected_B2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_24hr_MOI_20_infected_B2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_24hr_MOI_20_infected_B4.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/20230418_MB-6206_24hr_Uninfected_B4.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073167/Maxqaunt_search.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["nichollas.scott@unimelb.edu.au"],"submitter":["Nichollas Scott"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Burkholderia cenocepacia","Opsonization","Dual-proteomics","Proteomics","Burkholderia","Macrophages","Data-independent acquisition"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD073167"],"sample_protocol":["THP-1 macrophages were collected using ice cold dissociation buffer, centrifuged at 300 xg for 5 minutes at 4°C and then lysed in 200 μL 4% SDC in 100 mM of Tris-HCl (pH 8.5) at 95°C for at least 10 minutes with shaking at 2000 rpm. BCA assays were performed to quantify the total protein from lysates and 100 μg of protein used for proteomic analysis. SDC solubilized samples were prepared according to the approach of Kulak et al.. Briefly, samples were reduced and alkylated using 20 mM tris(2-carboxyethyl)phosphine / 50 mM Chloroacetamide at 45°C for 30 minutes with shaking at 1500 rpm in the dark (Eppendorf Thermomixer). Trypsin was added in a 1:100 ratio with 1 µg of SOLu-trypsin (Sigma-Aldrich) added to each sample and digestion allowed to proceed for 18 hours at 37°C with shaking at 600 rpm. Trypsin digestion was quenched by the addition of 1.25x volumes of 100% isopropanol and 0.115x volumes of 10% trifluoroacetic acid (TFA) to each sample with the resulting peptides extracted using styrenedivinyl benzene-reverse phase sulfonate (SDB-RPS) (Sigma-Aldrich) StageTips. The resulting SDB-RPS columns were washed with 150 µL 100% acetonitrile (ACN), followed by 150 µL of 30% methanol and 1% TFA by centrifugation at 1000 xg for 5 minutes. Columns were equilibrated with 150 µL of 1% TFA followed by 150 µL of 90% isopropanol and 1% TFA. Samples were loaded onto columns then washed with 150 µL of 90% isopropanol and 1% TFA, followed by 150 µL of 90% ethyl acetate and 1% TFA, then washed with 150 µL of 1% TFA before being eluted with 150 µL of 80% ACN and 5% ammonium hydroxide. Peptides were dried and stored at -20°C till analysis. Four biological replicates were prepared for each group to allow statistical analysis.  Prepared C18 purified peptides from each sample were re-suspended in Buffer A* (2% acetonitrile, 0.01% trifluoroacetic acid) and separated using a two-column chromatography setup composed of a PepMap100 C18 20-mm by 75-m trap and a PepMap C18 500-mm by 75-m analytical column using a Dionex Ultimate 3000 UPLC (Thermo Fisher Scientific). Each sample was concentrated onto the trap column at 5 l/min for 6 min with Buffer A (0.1% formic acid, 2% DMSO) before being subjected to analytical separation at 300 nl/minute. Samples were analysed using a 185-minute analytical runs by altering the buffer composition from 3% Buffer B to 25% B over 172 minutes, then from 25% B to 40% B over 4 minutes, then from 40% B to 80% B over 1 minute. The composition was held at 80% B for 3 minutes, and then dropped to 3% B over 1 minute before being held at 3% B for another 4 minutes. DDA experiments were performed with a single MS1 event (70k resolution, AGC 3x106, 375-1400 m/z) and up to 15 MS2 scans (HCD, NCE 28:32:32%, 35k resolution, AGC 2x105 and a maximal injection time of 110 ms)."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["DDA datasets were searched using MaxQuant version 2.2.0.0 against the B. cenocepacia K56-2 proteome (UniProt accession: UP000011196, 7467 proteins) and B. cenocepacia strain J2315 proteome (UniProt accession: UP000001035, 6993 proteins) to enable the matching of J2315 gene accessions, as well as the human proteome (UniProt accession: UP000005640). Carbamidomethyl was set as a fixed modification, and Acetyl (Protein N-term) as well as Oxidation (M) allowed as variable modifications. Searches were undertaken with both the LFQ and \"Match Between Run\" options enabled. Log2(x) transformation, Z-score normalization and statistical analysis was undertaken using Perseus v1.6.07 with missing values imputed based on the total observed protein intensities with a range of 0.3 σ and a downshift of 2.5 σ. Biological replicates were grouped together and Student's t-tests used to compare individual groups excluding fold changes less then +/- 1 log2. Multiple hypothesis correction was undertaken using a permutation-based FDR approach allowing an FDR of 1%."],"omics_type":["Proteomics"],"labhead":["Nichollas E. Scott"],"instrument_platform":[""],"labhead_affiliation":["Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["nichollas.scott@unimelb.edu.au"],"publication":["Not available"],"submitter_affiliation":["University of Melbourne"],"submitter_country":["Australia"],"additional_accession":[]},"is_claimable":false,"name":"Opsonisation improves duel proteomic analysis of Burkholderia cenocepacia infections. -DDA infection","description":"The opportunistic Cystic Fibrosis (CF) pathogen Burkholderia cenocepacia is associated with severe lung infections. Within the CF lung, macrophages are both a crucial reservoir and a key mediator of the intense inflammatory response characteristic of B. cenocepacia infections. Despite the importance of macrophages for B. cenocepacia pathogenesis, there is a paucity of insight into how B. cenocepacia internalisation and replication impacts both the host and B. cenocepacia proteomes. A key limitation for understanding the proteomic changes during intracellular replication of B. cenocepacia has been the low infectivity of this pathogen, resulting in the generation of mixed cell populations dominated by uninfected cells within in vitro models. Using antibody-mediated opsonization, we show that by improving the efficiency and uniformity of B. cenocepacia internalization this enhances dual proteomic analysis. Comparing opsonized and non-opsonized infections, we show that changes in both host and internalized B. cenocepacia can be assessed in a single experimental framework. At the proteome level, opsonization dramatically improves the detection of protein changes, enhancing the detection of pro-inflammatory signaling and macrophage activation markers. Utilizing this dual proteomic approach, we assess the impact of the B. cenocepacia type 6 secretion system (T6SS) and the T6SS effector TecA at 3 and 24 hours post infection demonstrating that the presence/activities of the T6SS or TecA do not greatly modulate the proinflammatory response of THP-1 cells. Thus, this work demonstrates a simple means for enhancing proteomic analysis of B. cenocepacia infections enabling dual proteomic 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