Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD055782/PRF_Q_2022_K_DESC_751_52162.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD055782/PRF_Q_2022_K_DESC_779_52810.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD055782/PRF_Q_2022_K_DESC_779_52813.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD055782/PRF_Q_2021_K_DESC_683_51599.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD055782/PRF_Q_2022_K_DESC_751_52161.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD055782/PRF_Q_2021_K_DESC_683_51605.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD055782/PRF_Q_2021_K_DESC_683_51599.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD055782/PRF_Q_2021_K_DESC_683_51605.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD055782/PRF_Q_2022_K_DESC_751_52161.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD055782/PRF_Q_2022_K_DESC_751_52162.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD055782/PRF_Q_2022_K_DESC_779_52810.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD055782/PRF_Q_2022_K_DESC_779_52813.rawprimaryOK200kdesch@med.umich.eduKarl DeschMass SpectrometryBottom-up proteomicsThrombosisStabilin-2ThrombosisTurboidhttps://www.ebi.ac.uk/pride/archive/projects/PXD055782Early Embryonic CellStreptavidin beads (prepared as described in the methods) were resuspended in 50μl 0.1M ammonium bicarbonate buffer (pH~8). Cysteines were reduced by the addition of 50μl 10 mM DTT, for 30 minutes at 45⁰C. Samples were cooled to room temperature, alkylation of cysteines was achieved by incubation with 65 mM 2-Chloroacetamide in the dark, for 30 minutes at room temperature. Overnight digestion with 1 ug sequencing grade modified trypsin was carried out at 37⁰C with constant shaking in a Thermomixer. Digestion was stopped by acidification and peptides were desalted using SepPak C18 cartridges according to the manufacturer’s protocol (Waters). Samples were then completely dried using a vacufuge. The resulting peptides were dissolved in 9μl of 0.1% formic acid/2% acetonitrile solution and 2μl of the peptide solution was resolved on a nano-capillary reverse phase column (Acclaim PepMap C18, 2 micron, 50 cm, ThermoScientific) using a 0.1% formic acid/2% acetonitrile (Buffer A) and 0.1% formic acid/95% acetonitrile (Buffer B) gradient at 300 nl/min over a period of 180 min (2-25% buffer B in 45 min, 25-40% in 5 min, 40-90% in 5 min followed by holding at 90% buffer B for 5 min and requilibration with Buffer A for 30 min). Eluent was directly introduced into a Q exactive HF mass spectrometer (Thermo Scientific, San Jose CA) using an EasySpray source. MS1 scans were acquired at 60K resolution (AGC target=3x106; max IT=50 ms). Data-dependent collision induced dissociation MS/MS spectra were acquired using the Top speed method (3 seconds) following each MS1 scan (NCE ~28%; 15K resolution; AGC target 1x105; max IT 45 ms).PrideProteins were identified by searching the MS/MS data against Homo sapiens (sp_canonical TaxID=9606) (v2024-03-27), 20291 reviewed entries; downloaded on 13th December 2021, appended with TurboID sequence, using Proteome Discoverer (v2.4, Thermo Scientific). Search parameters included MS1 mass tolerance of 10 ppm and fragment tolerance of 0.2 Da; two missed cleavages were allowed; carbamidomethylation of cysteine was considered fixed modification and oxidation of methionine, deamidation of asparagine and glutamine were considered as potential modifications. False discovery rate (FDR) was determined using Percolator and proteins/peptides with a FDR of ≤1% were retained for further analysis.ProteomicsKarl DeschUniversity of Michigan, Department of Pediatrics, 1150 W Medical Center Dr, MSRB III Bldg, Room 8315, Ann Arbor, MI 48109PARTIALHomo Sapiens (human)kdesch@med.umich.edu39970990 Underwood M, Da Veiga Leprevost F, Basrur V, Nesvizhskii AI, Rawley O, Golden K, Emmer B, Lillicrap D, Desch K. Identification of multiple novel procoagulant plasma ligands for stabilin-2. J Thromb Haemost. 2025 23(5):1622-1635 10.1016/j.jtha.2025.01.023University of MichiganUnited States<h4>Background</h4>Damaging STAB2 gene variants are associated with increased venous thromboembolic risk. STAB2 encodes stabilin-2, a clearance receptor, expressed by the liver and spleen. Given its function, it is likely that the prothrombotic state associated with stabilin-2 deficiency is due to reduced procoagulant protein clearance, but the identity of these ligands is unknown.<h4>Objectives</h4>To identify plasma stabilin-2 ligands using proximity biotinylation proteomics.<h4>Methods</h4>Cells stably expressing stabilin-2-TurboID were incubated with human plasma and biotin to initiate TurboID labeling of plasma ligands in endocytic vesicles. Biotinylated proteins were purified and identified using mass spectrometry. Candidate plasma ligands with roles in hemostasis were fluorescently labeled and incubated with stabilin-2 expressing and control cells. Flow cytometry assessed ligand surface binding and confocal microcopy assessed colocalization with stabilin-2 and lysosomes. Furthermore, plasma levels of ligands were measured in Stab2-deficient mice and littermate controls.<h4>Results</h4>Twenty-eight stabilin-2 specific ligands were identified. Interactions with von Willebrand factor, fibrinogen, pro(thrombin), heparin cofactor II, high molecular weight kininogen, plasminogen, and C4b-binding protein were probed. Heparin cofactor II, high molecular weight kininogen, plasminogen, and fibrinogen showed binding to stabilin-2 using flow cytometry (>2-fold higher than controls). Confocal microscopy demonstrated stabilin-2 dependent colocalization of all ligands with lysosomes. In Stab2-deficient mice, ligand levels were not significantly increased, suggesting in mice stabilin-2 is not their main clearance receptor.<h4>Conclusion</h4>These results confirm the value of proximity labeling proteomics in identifying receptor ligands and suggest damaging STAB2 variants may increase venous thromboembolic risk potentially through altered hemostatic protein clearance.Identification of multiple novel procoagulant plasma ligands for stabilin-2.Underwood Mary M, Da Veiga Leprevost Felipe F, Basrur Venkatesha V, Nesvizhskii Alexey I AI, Rawley Orla O, Golden Krista K, Emmer Brian B, Lillicrap David D, Desch Karl KfalseStabilin-2 is a clearance receptor for multiple procoagulant plasma ligands Short title: Stabilin-2 plasma ligandsDamaging STAB2 gene variants are associated with increased venous thromboembolic risk. STAB2 encodes stabilin-2, a clearance receptor, expressed by the liver and spleen. Given its function, it is likely that the prothrombotic state associated with stabilin-2 deficiency is due to reduced procoagulant protein clearance, but the identity of these ligands is unknown. We aimed to identify plasma stabilin-2 ligands using proximity biotinylation proteomics. Cells stably expressing stabilin-2-TurboID were incubated with human plasma and biotin to initiate TurboID labeling of plasma ligands in endocytic vesicles. Biotinylated proteins were purified and identified using mass spectrometry. Candidate plasma ligands with roles in hemostasis were fluorescently labeled and incubated with stabilin-2 expressing and control cells. Flow cytometry assessed ligand surface binding and confocal microcopy assessed colocalization with stabilin-2 and lysosomes. Furthermore, plasma levels of these ligands were measured in Stab2 deficient mice and littermate controls. Twenty-eight stabilin-2 specific ligands were identified. Interactions with von Willebrand factor (VWF), fibrinogen, pro(thrombin), heparin cofactor II (HCII), high molecular weight kininogen (HMWK), plasminogen and C4b binding protein (C4bp) were probed. HCII, HMWK, plasminogen and fibrinogen showed binding to stabilin-2 using flow cytometry (>2-fold higher than controls). Confocal microscopy demonstrated stabilin-2 dependent colocalization of all ligands with lysosomes. In Stab2 deficient mice, ligand levels were not significantly higher than wild type, suggesting in mice stabilin-2 is not their main clearance receptor. These results confirm the value of proximity labeling proteomics in identifying receptor ligands and suggest damaging STAB2 variants increase venous thromboembolic risk through altered clearance of hemostatic 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