Exploring the Mitochondrial Degradome by the TAILS Proteomics Approach in a Cellular Model of Parkinson's Disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31417398", "kind": "science-record", "revision": 8, "content_hash": "sha256:bf222420be59b259baac2a50dc38f14783b9f669beb491204ce0ea603192003f", "created_at": "2026-11-01T15:40:48Z", "updated_at": "2026-11-01T22:44:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the Mitochondrial Degradome by the TAILS Proteomics Approach in a Cellular Model of Parkinson's Disease.", "doi": "10.3389/fnagi.2019.00195", "pmid": "31417398", "authors": ["Marta Lualdi", "Maurizio Ronci", "Mara Zilocchi", "Federica Corno", "Emily S Turilli", "Mauro Sponchiado", "Antonio Aceto", "Tiziana Alberio", "Mauro Fasano"], "journal": "Frontiers in aging neuroscience", "year": 2019, "abstract": "Parkinson's disease (PD) is the second most frequent neurodegenerative disease worldwide and the availability of early biomarkers and novel biotargets represents an urgent medical need. The main pathogenetic hallmark of PD is the specific loss of nigral dopaminergic neurons, in which mitochondrial dysfunction plays a crucial role. Mitochondrial proteases are central to the maintenance of healthy mitochondria and they have recently emerged as drug targets. However, an exhaustive characterization of these enzymes and their targets is still lacking, due to difficulties in analyzing proteolytic fragments by bottom-up proteomics approaches. Here, we propose the \"mitochondrial dimethylation-TAILS\" strategy, which combines the isolation of mitochondria with the enrichment of N-terminal peptides to analyze the mitochondrial N-terminome. We applied this method in a cellular model of altered dopamine homeostasis in neuroblastoma SH-SY5Y cells, which recapitulates early steps of PD pathogenesis. The main aim was to identify candidate mitochondrial proteases aberrantly activated by dopamine dysregulation and their cleaved targets. The proposed degradomics workflow was able to improve the identification of mitochondrial proteins if compared to classical shotgun analysis. In detail, 40% coverage of the mitochondrial proteome was obtained, the sequences of the transit peptides of two mitochondrial proteins were unveiled, and a consensus cleavage sequence for proteases involved in the processing of mitochondrial proteins was depicted. Mass spectrometry proteomics data have been submitted to ProteomeXchange with the identifier PXD013900. Moreover, sixty-one N-terminal peptides whose levels were affected by dopamine treatment were identified. By an in-depth analysis of the proteolytic peptides included in this list, eleven mitochondrial proteins showed altered proteolytic processing. One of these proteins (i.e., the 39S ribosomal protein L49 - MRPL49) was cleaved by the neprilysin protease, already exploited in clinics as a biotarget. We eventually demonstrated a mitochondrial subcellular localization of neprilysin in human cells for the first time. Collectively, these results shed new light on mitochondrial dysfunction linked to dopamine imbalance in PD and opened up the possibility to explore the mitochondrial targets of neprilysin as candidate biomarkers.", "claims": [{"id": "claim-method", "statement": "Statistical significance was verified by either two-tailed t-test or two-way ANOVA.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31417398", "locator": "sections[5] \"SDS-PAGE and Western Blotting\" paragraph 3", "quote": "Statistical significance was verified by either two-tailed t-test or two-way ANOVA."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated for this study can be found in the ProteomeXchange (Accession: PXD013900; PWD: cicciociccio).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31417398", "locator": "sections[17] \"Data Availability\" paragraph 2", "quote": "The datasets generated for this study can be found in the ProteomeXchange (Accession: PXD013900; PWD: cicciociccio)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31417398"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_unresolved", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD013900"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD013900"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_unresolved"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31417398", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fnagi.2019.00195", "sha256": "sha256:15dfe4f39fc2a2f4ad8286fecc27811fe60522e2882e6337bc1424f21321b300", "bytes": 57227, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fnagi.2019.00195", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6685049", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD013900", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD013900", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD013900", "version": null, "note": "The datasets generated for this study can be found in the ProteomeXchange (Accession: PXD013900; PWD: cicciociccio).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated for this study can be found in the ProteomeXchange (Accession: PXD013900; PWD: cicciociccio).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31417398:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a1c11053f905c0f67536021e7f296c640c9b3e59420d49f937e0b3e927cded39", "bytes": 405, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T1", "version": null, "note": "Newly identified mtTP removal sites.", "structure": {"pmcid": "PMC6685049", "section_index": 13, "section_title": "Characterization of the Mitochondrial N-Terminome", "row_count": 3, "column_count": 5}, "table": {"label": "TABLE 1", "caption": "Newly identified mtTP removal sites.", "rows": [["Protein", "Identified N-term", "P′ position", "mtTP", "Chain"], ["Threonine-tRNA ligase (Q9BW92)", "LHTAVVSTPPR", "20", "1–19", "20–718"], ["28S ribosomal protein S35 (P82673)", "STAVYSATPVPTPSLPER", "23", "1–22", "23–323"]], "row_count": 3, "column_count": 5, "numeric_cells": 8, "header_rows": 1, "locator": "section[13]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:31417398:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4609def362071c2d56fefb50a4a93ebc98cbc979126661e70f955ee8fbbd8fdf", "bytes": 1678, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T2", "version": null, "note": "N-terminal peptides OVER-represented in DA vs. CTRL (n=24).", "structure": {"pmcid": "PMC6685049", "section_index": 14, "section_title": "Effects of Altered DA Homeostasis on Mitochondrial N-Terminome", "row_count": 25, "column_count": 4}, "table": {"label": "TABLE 2", "caption": "N-terminal peptides OVER-represented in DA vs. CTRL (n=24).", "rows": [["N-term peptide sequence", "Protein*", "Type of N-term", "DA/CTRL (log2) ± SEM"], ["SDMPPLTLEGIQDR", "O14561", "TP-removal", "1.25 ± 0.44"], ["LHLGVTPSVIR", "O14773", "TP-removal", "DA only∗∗"], ["STQAATQVVLNVPETR", "O75439", "“ragging” TP-removal", "0.92 ± 0.26"], ["SSEAPPLINEDVKR", "P04843", "“ragging” TP-removal", "0.65 ± 0.05"], ["DAPEEEDHVLVLR", "P07237", "TP-removal", "0.98 ± 0.24"], ["AKDVKFGADAR", "P10809", "TP-removal", "0.72 ± 0.04"], ["VNFTVDQIR", "P13639", "Met-removal", "0.67 ± 0.07"], ["DDEVDVDGTVEEDLGKSR", "P14625", "TP-removal", "DA only∗∗"], ["KEAESSPFVER", "P14625", "Internal", "DA only∗∗"], ["ASGANFEYIIAEKR", "P30084", "TP-removal", "0.69 ± 0.08"], ["SDVLELTDDNFESR", "P30101", "TP-removal", "1.29 ± 0.45"], ["DDLVTVKTPAFAESVTEGDVR", "P36957", "TP-removal", "0.77 ± 0.14"], ["VLLESEQFLTELTR", "P37108", "Met-removal", "0.67 ± 0.09"], ["DGVGGDPAVALPHR", "P49257", "TP-removal", "1.09 ± 0.42"], ["LRPGDCEVCISYLGR", "P55145", "TP-removal", "DA only∗∗"], ["SASVVSVISR", "P61803", "Met-removal", "0.71 ± 0.08"], ["ESETTTSLVLER", "Q04837", "TP-removal", "0.75 ± 0.07"], ["VMEKPSPLLVGR", "Q13283", "Met-removal", "0.77 ± 0.05"], ["LSQTQGPPDYPR", "Q13405", "Internal", "0.80 ± 0.09"], ["AAVAATAAAKGNGGGGGR", "Q6Y1H2", "Met-removal", "0.67 ± 0.07"], ["AATLILEPAGR", "Q86TX2", "Met-removal", "0.67 ± 0.07"], ["AADTQVSETLKR", "Q92616", "Met-removal", "0.84 ± 0.19"], ["RASPAGGPLEDVVIER", "Q96AY3", "“ragging” TP-removal", "0.84 ± 0.16"], ["SEVPGAAAEGSGGSGVGIGDR", "Q9NPA0", "TP-removal", "0.79 ± 0.21"]], "row_count": 25, "column_count": 4, "numeric_cells": 42, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:31417398:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d81caac98b520e3fe4b4418f8567fd0b5b1510ac33af67157b9997114516b302", "bytes": 2556, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#T3", "version": null, "note": "N-terminal peptides UNDER-represented in DA vs. CTRL (n=37).", "structure": {"pmcid": "PMC6685049", "section_index": 14, "section_title": "Effects of Altered DA Homeostasis on Mitochondrial N-Terminome", "row_count": 38, "column_count": 4}, "table": {"label": "TABLE 3", "caption": "N-terminal peptides UNDER-represented in DA vs. CTRL (n=37).", "rows": [["N-term peptide sequence", "Protein*", "Type of N-term", "DA/CTRL (log2) ± SEM"], ["VHQSVATDGPSSTQPALPKAR", "O75251", "“ragging” TP-removal", "CTRL only∗∗"], ["LAADVGKAGAER", "P05141", "Internal", "−1.65 ± 0.60"], ["GNLANVIR", "P05141", "Internal", "CTRL only∗∗"], ["AQTSPSPKAGAATGR", "P06576", "TP-removal", "−0.70 ± 0.12"], ["EICGPGIDIR", "P08069", "TP-removal", "CTRL only∗∗"], ["MAPEVLPKPR", "P09669", "Natural", "−0.87 ± 0.26"], ["APEVLPKPR", "P09669", "“ragging” TP-removal", "−0.70 ± 0.12"], ["TSTAPAASPNVR", "P11498", "“ragging” TP-removal", "−0.72 ± 0.08"], ["LAADVGKSGTER", "P12236", "Internal", "−2.57 ± 0.67"], ["NQSPVDQGATGASQGLLDR", "P18827", "Internal", "−0.72 ± 0.08"], ["SHGSQETDEEFDAR", "P20674", "TP-removal", "−0.74 ± 0.15"], ["VAHFTFQPDPEPR", "P21953", "TP-removal", "CTRL only∗∗"], ["VSKPTLKEVVIVSATR", "P24752", "TP-removal", "−0.74 ± 0.11"], ["QKTGTAEMSSILEER", "P25705", "TP-removal", "−0.69 ± 0.10"], ["AIAAKEKDIQEESTFSSR", "P42704", "TP-removal", "−0.69 ± 0.08"], ["ADCISEPVNR", "P43304", "TP-removal", "−1.35 ± 0.27"], ["SHTDIKVPDFSEYR", "P47985", "TP-removal", "CTRL only∗∗"], ["MKEGMSNNSTTSISQAR", "P50150", "Met-removal", "−0.81 ± 0.15"], ["APSVPAAEPEYPKGIR", "P54819", "Met-removal", "−0.66 ± 0.05"], ["SVPAAEPEYPKGIR", "P54819", "“ragging” TP-removal", "CTRL only∗∗"], ["GVQVETISPGDGR", "P62942", "Met-removal", "−0.59 ± 0.16"], ["STAVYSATPVPTPSLPER", "P82673", "TP-removal (new)", "−0.71 ± 0.11"], ["SETTTSLVLER", "Q04837", "“ragging” TP-removal", "CTRL only∗∗"], ["TVNSLNVSANEN", "Q13740", "Internal", "CTRL only∗∗"], ["AELPPVPGGPR", "Q14249", "TP-removal", "CTRL only∗∗"], ["STNVQKEGQGSQTLR", "Q6PML9", "Internal", "−0.70 ± 0.06"], ["GAPEVLVSAPR", "Q7Z4H8", "TP-removal", "−0.73 ± 0.12"], ["GGSCPHPSSAPR", "Q8WY21", "TP-removal", "CTRL only∗∗"], ["STLQEVVGIR", "Q969P0", "Internal", "CTRL only∗∗"], ["EEQPPETAAQR", "Q96HE7", "TP-removal", "−0.68 ± 0.07"], ["HGEEQPPETAAQR", "Q96HE7", "“ragging” TP-removal", "CTRL only∗∗"], ["SAPGEDEECGR", "Q99523", "Propeptide-removal", "CTRL only∗∗"], ["TTFNIQDGPDFQDR", "Q99757", "TP-removal", "−0.72 ± 0.12"], ["LHTAVVSTPPR", "Q9BW92", "TP-removal (new)", "CTRL only∗∗"], ["YSKSPSNKDAALLEAAR", "Q9H078", "Internal", "CTRL only∗∗"], ["LHTAANAAATATETTCQDVAATPVAR", "Q9NP92", "Internal", "−0.72 ± 0.08"], ["SCPGTVAKDLR", "Q9NVV4", "“ragging” TP-removal", "CTRL only∗∗"]], "row_count": 38, "column_count": 4, "numeric_cells": 55, "header_rows": 1, "locator": "section[14]/table-wrap[2]#T3"}}], "gaps": ["asset:data:geo:PXD013900 not downloaded", "asset:data:geo:PXD013900 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Statistical significance was verified by either two-tailed t-test or two-way ANOVA."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["PXD013900"], "resolved_accessions": [], "statements": ["The datasets generated for this study can be found in the ProteomeXchange (Accession: PXD013900; PWD: cicciociccio)."], "basis": "The paper names PXD013900, but the accession does not resolve in the repository (not_in_proteomexchange), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:31417398", "data:geo:PXD013900", "asset:table:pmid:31417398:1", "asset:table:pmid:31417398:2", "asset:table:pmid:31417398:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD013900"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:15:55Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 41055, "completion_tokens": 1341, "cached_tokens": 792}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:31417398", "type": "paper", "label": "pmid:31417398"}, {"id": "source:pmid:31417398", "type": "manuscript", "label": "PMID 31417398 full text"}, {"id": "data:geo:PXD013900", "type": "dataset", "label": "GEO PXD013900"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31417398", "type": "paper", "label": "pmid:31417398"}, {"id": "source:pmid:31417398", "type": "manuscript", "label": "PMID 31417398 full text"}, {"id": "data:geo:PXD013900", "type": "dataset", "label": "GEO PXD013900"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31417398", "type": "extraction", "used": ["source:pmid:31417398"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD013900", "type": "accession_resolution", "used": ["data:geo:PXD013900"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:31417398", "parent_hash": "sha256:ed27fe70eaf6dccc980368c74b825ef60d5cc4f28cd6b94f2d0765a634fc04a8", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD013900 licence not read", "asset:data:geo:PXD013900 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_unresolved"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ing the Mitochondrial Degradome by the TAILS Proteomics Approach in a Cellular Model of Parkinson's", "analyzing proteolytic fragments by bottom-up proteomics approaches. Here, we propose the \"mitochondr", "ial proteins was depicted. Mass spectrometry proteomics data have been submitted to ProteomeXchange", "sing of mitochondrial proteins was depicted. Mass spectrometry proteomics data have been submitted to Prote"], "order_basis": "paper_text_order:6", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ltered dopamine homeostasis in neuroblastoma SH-SY5Y cells, which recapitulates early steps of PD", "t 37°C in a 5% CO2 humidified atmosphere and cultured in Dulbecco’s modified Eagle’s medium (DMEM), s", "lture and Treatments The human neuroblastoma SH-SY5Y cells (ECACC General Collection, cat# 940303", "homeostasis. First, we treated neuroblastoma SH-SY5Y cells with dopamine and we isolated the mito"], "order_basis": "paper_text_order:1003", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Statistical significance was verified by either two-tailed t-test or two-way ANOVA."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}