{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD080067/ProteinGroups_Quantity_Report.xlsx"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD080067/checksum.txt"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD080067/2024_Human_cont_iRT.fasta"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD080067/20251023_215728_CAF_vs_wt_cells.sne","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD080067/Raw_data.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["helena.skalnikova@lf1.cuni.cz"],"submitter":["Jakub Cervenka"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","diaPASEF","Data-independent acquisition","Bottom-up proteomics"],"disease":["Lung Cancer","Brain Cancer"],"software":[""],"submitter_keywords":["Lc-ms","Cancer-associated fibroblasts","Extracellular matrix","Brain metastases","Cell migration","Primary cell culture"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD080067"],"tissue":["Brain","Primary Cell","Cell Culture","Fibroblast"],"sample_protocol":["For proteomic analyses, cell lysates were prepared from 6 cultures (L-BrM-CAF n = 3 and Subgalear-NF n = 3). Cells (4×105) were seeded into a 100 mm Petri dish, and grown until subconfluent. Then, the culture medium was aspirated, and the cell monolayer was washed twice with pre-warmed PBS (37 °C). Cells were then lysed by adding a lysis buffer (1% SDS in 50 mM Tris-HCl pH 7.5), pre-heated to 95 °C. Complete cell lysis was immediately verified under a microscope. Subsequently, the lysates were scraped, collected into microtubes, and incubated for additional 5 min at 95 °C to ensure complete protein denaturation. Finally, the samples were stored at −80 °C until further use. Cell lysates from L-BrM-CAFs (H131, NCH402, and NCH621) and Subgalear-NFs (NCH233, NCH379, and NCH434) were processed by our modified filter-aided sample preparation (FASP) (https://doi.org/10.1111/bpa.13265) with modifications. Briefly, Microcon 30 K centrifugal ultrafiltration units (Merck) were pre-washed with water, and 30 µg of protein per sample were loaded onto the units. The ultrafiltration units were then washed three times with a wash buffer (8 M urea and 5 mM EDTA in 50 mM ammonium bicarbonate) by centrifugation at 13,000 g for 20 min at 22°C. Subsequently, proteins were reduced with 10 mM tris(2-carboxyethyl) phosphine in the wash buffer (30 min at 32°C) and alkylated with 40 mM iodoacetamide in the wash buffer (30 min at 25°C, in the dark). Finally, the ultrafiltration units were washed once with the wash buffer and three times with 50 mM ammonium bicarbonate, and centrifuged (14,000 g, 25 min, 22°C). On-filter digestion was performed with 0.6 µg of rLys-C protease (Promega) and 1 µg of Trypsin Platinum protease (Promega) in 50 mM ammonium bicarbonate containing 0.02% (w/v) ProteaseMAX (Promega) overnight at 37°C. Peptides were collected by centrifugation, acidified by formic acid to a final concentration of 2% (v/v), and centrifuged (14,000 g, 20 min, 4°C). The supernatants were desalted using Pierce peptide desalting spin columns (Thermo Scientific) according to manufacturer´s instructions, except formic acid was used instead of trifluoroacetic acid. Peptides were dried using a vacuum centrifuge at 45°C and resuspended in 0.1% formic acid in water. Peptide concentrations were measured at λ = 280 nm (Synergy HTX, BioTek). Samples were then diluted to 0.2 µg/µL in QuanRecovery with MaxPeak HPS vials (Waters) and spiked with indexed Retention Time (iRT) peptides (Biognosys) at iRT:sample ratio 1:30 (v/v). Peptide samples were loaded onto a trap column (PepMap Neo C18, 5 mm × 0.3 mm, 5 µm, Thermo Scientific) and subsequently separated on an analytical column (PepSep Ultra C18, 25 cm × 75 µm, 1.5 µm, Bruker Daltonics) using a linear gradient of 2-35% acetonitrile with 0.1% formic acid over 90 min at a flow rate 200 nL/min. The analytical column was maintained at 50°C. Liquid chromatography was performed using a nanoElute 2 system (Bruker Daltonics) coupled to a mass spectrometer timsTOF HT (Bruker Daltonics) with a CaptiveSpray 2 ion source. For data-dependent acquisition (DDA), 0.6 µg of peptides per sample was analyzed with the default method DDA PASEF-standard_1.1_sec_cycletime (1/K0 range of 0.6-1.6 V·s/cm2, ramp/accumulation time of 100 ms, 10 PASEF ramps per cycle, and a total cycle time 1.17 s) employed in positive ion mode with adjusted MS scan range of 300-1700 m/z. For data-independent acquisition (DIA), 0.6 µg of peptides per sample was analyzed with the default method dia-PASEF – long gradient (1/K0 range of 0.6-1.6 V·s/cm2, ramp/accumulation time of 100 ms, 16 MS/MS ramps, 32 MS/MS windows, and a cycle time 1.8 s) employed in positive ion mode with adjusted MS scan range of 300-1700 m/z."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Raw data were analyzed in Spectronaut (version 19.5.241126.62635, Biognosys). DIA data were processed by directDIA analysis workflow with default BGS Factory Settings with the following modifications. The corresponding DDA data were employed as library extension runs to create a hybrid spectral library. The protein FASTA database was compiled by merging the UniProtKB Homo sapiens reference proteome (release 2024_06, proteome updated on 07102024; one protein sequence per gene, in total 20,650 proteins), with the 381 universal contaminant proteins (https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00145), and the iRT sequence (Biognosys). Specific cleavage rule was used for combination of Lys-C and trypsin – always cleavage after lysine, and cleavage after arginine, unless proline proceeds. Two missed cleavages were allowed. Carbamidomethylation of cysteine was set as a fixed modification, and protein N-terminal acetylation and methionine oxidation were set as variable modifications. The Hybrid (DDA + DIA) Library option was selected in DIA Analysis Workflow in Experiment Settings. Data were normalized in Spectronaut using cross-run local normalization. No filter type and automatic row selection were applied. Proteins identified by a single stripped peptide sequence (single hit proteins) were excluded from further analysis. Differential protein abundance analysis was performed in Spectronaut Viewer (version 20.3.251119.92449, Biognosys) using an unpaired t-test. Statistically significant changes of protein abundances were considered for fold-change ≥ 1.5 and Qvalue ≤ 0.05."],"omics_type":["Proteomics"],"labhead":["Helena Kupcová Skalníková"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Laboratory of Proteomics, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, U Nemocnice 5, Prague 2, 128 00, Czech Republic"],"species":["Homo Sapiens (human)"],"submitter_mail":["jakub.cervenka@lf1.cuni.cz"],"publication":["42551489 Výmolová B, Pfeiferová L, Smetana TK, Výmola P, Ternerová N, Zubaľ M, Kolář M, Šáchová J, Gyönyörová S, Balážiová E, Houdová Megová M, Červenka J, Kupcová Skalníková H, Španko M, Smetana K, Lacina L, Netuka D, Tomáš R, Bušek P, Šedo A. Brain metastasis-associated fibroblasts shape the tumour microenvironment to enhance cancer cell invasion.  Brain Pathol. 2026:e70129 10.1111/bpa.70129"],"submitter_affiliation":["Laboratory of Proteomics, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic"],"submitter_country":["Czechia"],"pubmed_abstract":["Brain metastases (BrM) are a frequent and life-threatening complication of solid tumours, with lung cancer representing their most common source. While cancer-associated fibroblasts (CAFs) are well-established contributors to tumour progression in many extracranial malignancies, their presence and function within the brain tumour microenvironment, where fibroblasts have long been considered scarce or absent, remain poorly understood. Here, we isolated and characterised fibroblast-like cells from 13 human BrMs of diverse origins. These BrM-associated CAFs (BrM-CAFs) expressed canonical CAF markers and showed reduced proliferation and increased senescence compared to normal fibroblasts. Their transcriptome was enriched for extracellular matrix (ECM)-related genes, including multiple collagens, fibronectin, and matrix-remodelling enzymes. In vitro, BrM-CAFs produced a fibrillar ECM, and in BrM tissues, their abundance was associated with collagen I and fibronectin deposition. Transcriptomic, proteomic, and secretome analyses further revealed that BrM-CAFs produce multiple cytokines, chemokines, and growth factors that promote cell motility. BrM-CAF conditioned medium promoted both monocyte migration and the migration of cancer cells, including established cell lines and patient-derived lung cancer BrM cells; monocyte migration was partially reduced by inhibition of CCL2/CCR2 signalling, whereas blocking CXCL12, CXCL16, or CX3CL1 attenuated BrM-CAF-induced cancer cell migration. Beyond these effects on migration, exposure to BrM-CAFs increased cancer cell invasion in transwell and heterotypic 3D spheroid assays. In contrast, their effects on cancer cell proliferation were limited and did not indicate a growth-promoting role. Exposure to BrM-CAFs was also associated with increased expression of interferon-stimulated genes in cancer cells. Together, our findings support a role for BrM-CAFs in shaping the brain metastatic microenvironment through ECM remodelling and the secretion of pro-migratory mediators, promoting monocyte and cancer cell migration and enhancing cancer cell invasion. These data identify BrM-CAFs as active stromal participants in BrM biology and support further investigation of their biological, diagnostic, and therapeutic relevance."],"pubmed_title":["Brain metastasis-associated fibroblasts shape the tumour microenvironment to enhance cancer cell invasion."],"pubmed_authors":["Výmolová Barbora B, Pfeiferová Lucie L, Smetana Tadeáš Karel TK, Výmola Petr P, Ternerová Nikola N, Zubaľ Michal M, Kolář Michal M, Šáchová Jana J, Gyönyörová Soňa S, Balážiová Eva E, Houdová Megová Magdalena M, Červenka Jakub J, Kupcová Skalníková Helena H, Španko Michal M, Smetana Karel K, Lacina Lukáš L, Netuka David D, Tomáš Robert R, Bušek Petr P, Šedo Aleksi A"],"additional_accession":[]},"is_claimable":false,"name":"Whole-proteome profiling of human lung cancer brain metastasis-associated fibroblasts","description":"Cancer-associated fibroblasts (CAFs) are increasingly recognized as an important component of the brain metastasis tumour microenvironment; however, their proteomic phenotype remains poorly characterized. This dataset contains mass spectrometry-based proteomic profiles of primary human brain metastasis-associated fibroblasts (BrM-CAFs) isolated from lung cancer brain metastases (L-BrM-CAF, n = 3) and control, non-tumorous subgalear fibroblasts (Subgalear-NF, n = 3). Whole-cell lysates were analyzed using data-independent acquisition (DIA) mass spectrometry, supported by a project-specific spectral library generated from data-dependent acquisition (DDA) measurements. The dataset was generated to characterize the molecular phenotype of BrM-CAFs and to investigate protein-level alterations associated with stromal activation, extracellular matrix remodelling, and tumour–stroma interactions. The data provide a resource for studies of the brain metastasis microenvironment and CAF 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