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Luca NegriMass SpectrometryBottom-up proteomicsOsteosarcomahttps://www.ebi.ac.uk/pride/archive/projects/PXD075484Cell CultureProtein extraction, cleaning, and trypsinization for global proteome analysis Once PDX models were dissociated using a tissue homogenizer and passed through both 18G and 22G needles as described previously, 5% of the fully fluid mixture was mixed with a detergent-based lysis buffer (500 mM Tris-Cl (pH 8.0), 50 mM NaCl, 40 mM 2-Chloroacetimide, 10 mM TCEP, 5 mM EDTA, 2% (v/v) SDS, 1% (v/v) NP-40, 1% (v/v) Triton X-100) at a 1:1 (v/v) ratio. The extraction, reduction and alkylation of proteins was facilitated in 1 step by incubation at 95 C for 90 minutes in a thermomixer with shaking at 1000 RPM. Following extraction, reduction and alkylation, the samples were cleaned as per the FASP protocol mentioned above to remove any incompatible reagents prior to quantification with the BCA assay. A total of 100 ug of material was aliquoted. Due to the use of a detergent-heavy lysis buffer, further cleaning of proteins was carried out using the Single-Pot, Solid Phase-enhanced Sample Preparation (SP3) protocol. Briefly, the carboxylate-functionalized magnetic beads (Cytiva) were washed briefly in HPLC-grade H2O prior to incubation with 100ug of each sample in the presence of 100% EtOH (final % = 50%) for 5 minutes at 24C with mixing at 1000 RPM. After capture, the magnetic beads + proteins were captured to the side of the tube using a magnet, and the supernatant containing contaminants was aspirated. The bead/protein mixture was washed 3 times with 80% EtOH, removing the supernatant between each wash after the beads were captured by said magnet. Finally, the bead:protein mixture was incubated with Trypsin/Lys-C at a 1:50 (trypsin:protein) ratio overnight at 37C with agitation (1000 RPM) in 50 mM HEPES (pH 8.0). The next day, the beads and undigested protein mixture was captured to the side of the tub with a magnet and the digested peptides were collected with the supernatant. Labelling of peptides using isobaric Tandem Mass Tags (TMT) for peptide quantification mass spectrometry and design of TMT plex TMT plexes were designed prior to labelling peptides to minimize the potential bias of running biological/technical replicates on the same plex. The TMT-11 plex (Thermo Scientific) was chosen for these studies, and each plex contained a SM channel, as well as a pooled internal standard (PIS) channel (equal amounts of all samples in the cohort (less SM samples)) which was used to normalize signal between different plexes post-analysis. TMT reagent was reconstituted in acetonitrile according to manufacturer’s recommendations and peptides were labelled with an excess of reagent (10 ul of TMT label per sample), incubated at room temperature for 30 minutes, and repeated for a total of 2 incubations. The labelling reaction was quenched by the addition of 10 mM glycine (Sigma Aldrich) to each sample then dried by half in a vacuum centrifuge. Samples were then combined into a single TMT plex and desalted using the stage-tipping protocol described elsewhere with 1 deviation; Due to the presence of SDC, samples required a centrifugation of 20,000 x G for 10 minutes following the addition of 0.1% Trifluoroacetic acid to remove the acid-labile SDC. The samples were dried fully in a vacuum centrifuge, and dried plexes were resuspended in 0.1% Formic Acid (Thermo Scientific) to be prepared for mass spectrometry analysis. A single deviation to the above methods was necessary for global proteome samples due to the higher yield of material. In brief, after the samples were combined into a single plex, the plexes were desalted using a Sep-Pak C-18 cartridge (50 mg binding capacity) (Waters) as per manufacturer’s recommendations and dried fully in vacuum centrifuge. High-pH reverse phase chromatography and offline fractionation of global proteome peptides Offline fractionation of global proteome samples was carried out precisely as described previously [PMID: 37812652] with no deviations. Nano LC-MS/MS data acquisition Data was collected on an Orbitrap Eclipse Tribrid mass spectrometer (Thermo Scientific) equipped with an Easy-nLC1000 (Thermo Scientific) by nano-electrospray chromatography using parameters described previously [PMID: 37812652] with no deviations. Data from surface and global proteome samples were collected simultaneously to ensure minimal batch effects, and data from both surface and global proteome plexes were collected in the same order.PrideNot availableRaw MS data were searched using Sequest HT algorithm through Proteome Discoverer suite (v2.4), against a human reference (2021/07/16 Swissprot; 20,351 sequences). Precursor and fragment mass tolerance were set at 10 ppm and 0.05 Da respectively. Dynamic modifications included Oxidation (+15.995 Da, M), Acetylation (+42.011 Da, N-Term). Static modification included Carbamidomethyl (+57.021 Da, C) and TMT (+229.163 Da, K, N-Term). Peptide-to-spectrum matches (PSMs) were filtered using Percolator by searching the results against a decoy sequence set, only PSMs with FDR < 1% were retained in the downstream analysis. PSMs were further filtered out if they had a signal-to-ratio (S/N) lower than 10 in the PIS channel and if they mapped to more than one unique protein. In order to normalize input signal, channel total intensity was scaled to 1e08. Each S/N was normalized to PIS channel (ratio) and, for each peptide, the median ratio of the 3 PSMs with the lowest isolation interference was used. Peptides were then median aggregated to the protein level. Proteins with at least 2 peptides were retained for downstream analysis, except in the surfaceome data were this filter was not applied. In order to estimate protein relative abundance, the S/N sum of the 3 highest abundance PSMs was taken and the average across channel was multiplied to S/N protein ratios obtained previously. In order to filter out mouse peptide/proteins from PDX samples, MS/MS data were searched again against a combined human (2021/07/16 Swissprot; 20,351 sequences) + mouse (2020/01/20 Swissprot, 17,057 sequences) reference proteome. The human+mouse combined search was used to determine which human proteins were assigned to proteins groups where a mouse protein was identified as the master protein by parsimony analysis performed by the Proteome Discoverer software.ProteomicsGregg MorinPARTIALCanada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada.Homo Sapiens (human)Not availablegnegri@bcgsc.caCanada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada.CanadafalseSurface and global proteome profiling of osteosarcoma patient derived xenograftsThis study analyzed 22 unique OS patient-derived xenografts (PDXs) using proteomics to identify surface proteins for potential immunotherapeutic targeting. Plasma membranes were enriched using density gradient ultracentrifugation and compared to a reference standard of 12 immortalized non-OS cell lines prepared in a similar manner. In parallel, global proteome analysis was carried out on all samples to place the identified surface proteins within the context of deregulated OS pathways. All models were analyzed by Tandem Mass Tags (TMT)-based mass spectrometry to quantify identified proteins.2026-07-282026-03-11PXD075484NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:190802NEWT:35554NEWT:9778NEWT:150475NEWT:9417NEWT:347515NEWT:1216979NEWT:307972NEWT:32046NEWT:544496NEWT:5180NEWT:256737NEWT:2042546NEWT:115104NEWT:1081927NEWT:67825NEWT:185579NEWT:43179NEWT:13076NEWT:1249668NEWT:376741NEWT:317NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:415540NEWT:876138NEWT:4081NEWT:554NEWT:98334NEWT:426428NEWT:237561NEWT:6928NEWT:10036NEWT:7574NEWT:1351NEWT:7215NEWT:29204NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:3885NEWT:746360NEWT:6239NEWT:3888NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:3641NEWT:383379NEWT:8782NEWT:1263854NEWT:1000589NEWT:1902NEWT:85962NEWT:160488NEWT:28104NEWT:317447NEWT:7955NCBITaxon:2NEWT:985076NEWT:7959NEWT:2261NEWT:4565NEWT:1264690NEWT:6192NEWT:28532NCBITaxon:38727NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:216595NEWT:243230NEWT:8355NEWT:1283NEWT:931281NEWT:1000561NEWT:9685NEWT:7029NEWT:1283300NEWT:6183NEWT:6063NEWT:334747NEWT:61235NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:725NEWT:360106NEWT:260707NEWT:287NEWT:10117NEWT:10239NCBITaxon:6191NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:83334NEWT:185431NEWT:83332NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:44685NEWT:2697049NEWT:1148NEWT:11676NEWT:55571NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:1123869NEWT:7370NEWT:75058NEWT:83906NEWT:607699NEWT:6282NEWT:1094343NEWT:208964NEWT:1134506NEWT:575584NEWT:296543NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:1182590NEWT:8726NEWT:6669NEWT:10090NEWT:935293NEWT:64152NEWT:749200NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:990346NEWT:5334NEWT:145953NEWT:257309NEWT:100816NEWT:230741NEWT:284812NCBITaxon:10359NCBITaxon:1313NEWT:43330NEWT:242619NEWT:44544NEWT:632957NEWT:373995NEWT:5689NEWT:645463NEWT:544404NEWT:3702NEWT:129249NEWT:9925NEWT:8839NEWT:4232NEWT:990119NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:421932NEWT:196627NEWT:408172NEWT:5691NEWT:408170NEWT:493760NEWT:260710NEWT:627025NEWT:400772NEWT:1097677NEWT:3708NEWT:128161NEWT:106592NEWT:1117957NEWT:9913NEWT:1432138NEWT:10312NEWT:1424507NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:8030NEWT:29722NEWT:380394NEWT:1692259NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:180066NEWT:67767NEWT:46835NEWT:135588NEWT:1843183NEWT:95486NEWT:58002NEWT:9103NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:146479NEWT:10306NCBITaxon:2759NEWT:1911079NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:3635NEWT:5811NEWT:235443NEWT:1480154NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:884019NEWT:169963NEWT:36329NEWT:1147787NCBITaxon:3044782NEWT:72407NEWT:9606NEWT:367830NEWT:157295NEWT:641501NEWT:178616NEWT:410289NEWT:373153NEWT:915099NEWT:74940NEWT:1450511NEWT:360094NEWT:470NEWT:84023NEWT:9838NCBITaxon:9615NEWT:58334NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:33952NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:178876NEWT:9940NEWT:327160NEWT:573NEWT:9031NEWT:1274420NEWT:7091NEWT:5784580000-0001-7722-8888