Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/File_mapping.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/evidence.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/summary.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/proteinGroups.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/parameters.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/mzRange.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/peptides.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/EZ-Link-Sulfo-NHS-S-CAMSites.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/Oxidation_M_Sites.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/msmsScans.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/msms.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/modificationSpecificPeptides.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/allPeptides.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/tables.pdfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/mqpar.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_Ctrl_CS_1_nr2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_Ctrl_CS_3_nr1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_CS_6_nr3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_Ctrl_CS_2_nr1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_CS_5_nr3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_CS_5_nr2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_CS_6_nr2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_Ctrl_CS_3_nr3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_CS_4_nr3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_Ctrl_CS_1_nr1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_Ctrl_CS_2_nr3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_CS_4_nr1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_Ctrl_CS_1_nr3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_CS_5_nr1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_CS_6_nr1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_Ctrl_CS_3_nr2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_CS_4_nr2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/180828_Pekka_Ctrl_CS_2_nr2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065511/search.zipprimaryOK200veli-matti.kahari@utu.fiPekka RappuData-dependent acquisitionMass SpectrometryBottom-up proteomicsSquamous Cell CarcinomaBiotinylationC1sSquamous cell cancerComplementhttps://www.ebi.ac.uk/pride/archive/projects/PXD065511Epithelial CellThe cells were biotinylated (EZ-link Sulfo-NHS-SS-Biotin (#21331, Thermo Fisher Scientific, Waltham, MA, USA), lyzed (50 mM Tris-HCl (pH 8.0), 120 mM NaCl, 2% Tergitol, 1% Triton X-100, 1% sodium deoxycholate, 100 µM oxidized glutathione, complete protease inhibitor tablet (Roche Diagnostics GmbH, Mannheim, Germany) and biotinylated proteins were immobilized with streptavidin beads (Streptavidin Sepharose TM High Performance Agarose beads (#71-5004-40 AE GE Healthcare Life Sciences, Uppsala, Sweden). After washing steps, cell surface proteins were eluted from the streptavidin beads in 50 mM DTT in 50 mM Tris-HCl pH 7.8 by incubating 40 min in +37 °C. The proteins were precipitated with ice cold asetone by incubating the samples o/n in -20 °C. Mass spectrometry-based proteomics The acetone-precipitated samples were dissolved in 100 µl of 8 M urea / 2 M thiourea in 100 mM ammonium bicarbonate, and the protein concentration was measured by Pierce 660 nm Protein Assay Reagent (Thermo Fisher Scientific). The cysteines were reduced by addition of dithiothreitol to 10 mM and incubation at 37 °C for 1 h and alkylated by addition of iodoacetamide to 35 mM and incubation at room temperature in dark for for 30 min. The remaining iodoacetamide was exhausted by addition of dithiothreitol to 25 mM. trypsin/LysC mixture (Promega) was added to enzyme:protein mass ratio of 1:50 and the samples were incubated at 37 °C for 4 h. The sample was diluted 1:8 by addition of 100 mM Tris-Cl, pH 8.5, trypsin/LysC mixture was added to enzyme:protein mass ratio of 1:50, and the samples were incubated 37 °C overnight. The resulting peptide solution was acidified with 1% trifluoroacetic acid to a pH of 2-3, followed by desalting with house-made Stage tips (Rappsilber J, Ishihama Y, Mann M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem. 2003 Feb 1;75(3):663-70. doi: 10.1021/ac026117i. PMID: 12585499) . Desalted peptides were vacuum dried, dissolved in 0.1 % formic acid and analyzed by LC-MS/MS. Equal amounts of peptides of each sample were loaded on a nanoflow HPLC system (Easy-nLC1000, Thermo Fisher Scientific, Waltham, Massachusetts, USA) coupled to a Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Fisher Scientific, Waltham, Massachusetts, USA) equipped with a nano‐electrospray ionization source. The peptides were first loaded on a trapping column and subsequently separated inline on a 15 cm C18 column (75 µm x 15 cm, ReproSil-Pur 5 µ;m 200 Å C18-AQ, Dr. Maisch HPLC GmbH, Ammerbuch-Entringen, Germany). The mobile phase consisted of 0.1% formic acid (solvent A) and acetonitrile/water (95:5 (v/v)) with 0.1% formic acid (solvent B). The peptides were separated with a 50 min gradient from 8 to 35 % of solvent B. Before the end of the run, the percentage of solvent B was raised to 100 % in 5 min and kept there for 5 min. Full MS scan over the mass-to-charge (m/z) range of 300-1750 with a resolution of 120,000 followed by data dependent acquisition of with an isolation window of 2.0 m/z and a dynamic exclusion time of 30 s was performed. The top 12 ions were fragmented by higher energy collisional dissociation (HCD) with a normalized collision energy of 27 and scanned over the m/z range of 200-2000 with a resolution of 15,000. After the MS2 scan for each of the top 12 ions had been obtained, a new full mass spectrum scan was acquired and the process repeated until the end of the 60-min run. Three repeated runs per sample were performed.PrideTandem mass spectra were searched against a database containing reviewed (SwissProt) human sequences of UniProtKB release 2022_04 using MaxQuant software version 1.6.10.43 (Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008 Dec;26(12):1367-72. doi: 10.1038/nbt.1511. Epub 2008 Nov 30. PMID: 19029910. ). Peptide-spectrum-match- and protein-level false discovery rates were set at 0.01. Carbamidomethyl (C), as a fixed modification, and oxidation (M) and reduced/carbamylated EZ-Link Sulfo-NHS-SS-Biotin (145.020 Da) of lysines as dynamic modifications were included. A maximum of two missed cleavages by trypsin/LysC was allowed. The LC-MS profiles were aligned, and the identifications were transferred to non-sequenced or non-identified MS features in other LC-MS runs (matching between runs). The protein was determined as detected in the sample if its identification had been derived from at least two unique or razor peptide identifications. MaxLFQ algorithm was used for quantitation.ProteomicsVeli-Matti KähäriPARTIALDepartment of Dermatology, University of Turku, Turku, FinlandHomo Sapiens (human)10.1038/S41389-026-00606-4pekka.rappu@utu.fiUniversity of TurkuFinlandfalseProteomic analysis of surface proteins from C1s siRNA-treated UT-SCC-59A squamous cell carcinoma cellsTo investigate the effect of C1s on cell surface proteins cSCC cell cultures were transfected with 120 nM control or C1s siRNAs and after 3 days incubation, the cells were biotinylated collected by streptavidin beads and subsequently analyzed by 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