{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD073587/PXD073587_community_annotated.sdrf.tsv"],"Xml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD073587/mqpar_w303.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD073587/mqpar.xml"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD073587/W303_R3_JC.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD073587/W303_R1_JC.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD073587/W303_R2_JC.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD073587/RRP46_R3_JC.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD073587/RRP46_R2_JC.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD073587/RRP6_R2_JC.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD073587/RRP6_R1_JC.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD073587/RRP46_R4_JC.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD073587/RRP6_R4_JC.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD073587/W303_Results_txt.rar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD073587/Rrp46_Rrp6_Results_txt.rar"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["ccoliv@iq.usp.br"],"submitter":["Felipe Almeida"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Affinity purification–mass spectrometry; phosphosite mapping; ssu processome; ribosome assembly factors;","ribosome assembly factors","phosphosite mapping","Affinity purification–mass spectrometry","ssu processome"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD073587"],"tissue":["Cell Culture"],"sample_protocol":["Yeast strains expressing TAP-tagged exosome subunits Rrp6 (RRP6-TAP::URA3) or Rrp46 (RRP46-TAP::HIS3) were grown in 6 L cultures of YPD medium at 30°C and harvested at log phase (OD₆₀₀ ≈ 1). Cell pellets from biological triplicates were resuspended in ice-cold extraction buffer (60 mM Tris-HCl pH 8.0, 50 mM NaCl, 10 mM MgCl₂, 5% glycerol, 1% Triton X-100, 1% PMSF, 1% EDTA, supplemented with protease and phosphatase inhibitor tablets) and flash-frozen in liquid nitrogen. Cell lysis was performed by cryogenic milling using a Retsch PM-100 Ball Mill. Lysates were clarified by ultracentrifugation at 28,100 rpm for 60 min at 4°C. For tandem affinity purification, clarified extracts were incubated for 2 h at 4°C with IgG-Sepharose 6 Fast Flow resin pre-equilibrated with extraction buffer. Beads were washed twice with extraction buffer and twice with 50 mM Tris-HCl / 50 mM NaCl wash buffer. Bound protein complexes were eluted on-column by overnight TEV protease cleavage at 4°C. Eluates were collected by gravity flow, lyophilized, and stored at –80°C. Lyophilized samples were resuspended in 8 M urea / 50 mM NH₄HCO₃ and reduced with 5 mM DTT at 56°C for 25 min. Alkylation was performed with 14 mM iodoacetamide for 30 min in the dark. Samples were diluted with 50 mM NH₄HCO₃ and digested with sequencing-grade trypsin (1:50, enzyme:substrate) for 16 h at 37°C. Digestion was quenched with 0.4% TFA and peptides were desalted using SepPak tC18 cartridges. Phosphopeptide enrichment was performed using the High-Select TiO₂ kit (Thermo Fisher Scientific). Tryptic peptides were loaded onto TiO₂ spin tips and processed according to the manufacturer’s protocol. Enriched phosphopeptides were vacuum-dried and stored at –80°C until LC–MS/MS analysis. Digested peptides were resuspended in 0.1% formic acid and fractionated on an reversed-phase capillary emitter column (10 cm × 75 μm, filled with 5 μm particle diameter C18 Aqua resins-Phenomenex) coupled to a nano-HPLC (Thermo). The fractionation was carried out through a 60 min gradient of 2–80% acetonitrile in 0.1% formic acid (buffer B) (0–28% of buffer B for 45 min, 28–80% for 13 min; 80–5% for 2 min) at a flow rate of 300 nl min−1.  The eluted peptides were analyzed by an LTQ-Orbitrap Velos (Thermo Scientific) (source voltage of 1.9 kV, capillary temperature of 200°C). The mass spectrometer was operated in DDA mode with dynamic exclusion enabled (exclusion duration of 45 seconds), MS1 resolution of 30,000, and MS2 normalized collision energy of 30. For each cycle, one full MS1 scan range of 200–2000 m/z was followed by ten MS2 scans (for the most intense ions) using an isolation window size of 1.0 m/z and collision-induced dissociation (CID). The 10 most intense ions were selected for fragmentation by CID in DDA. The .raw data from the LTQ Velos-Orbitrap were analyzed with the MaxQuant (version 2.6.7.0) software using the UniProt database (taxonomy Saccharomyces cerevisiae—strain ATCC 204508 / S288c), setting tolerance for the MS of 20 ppm and the MS/MS of 0.5 Da; carbamidomethylation of cysteine as a fixed modification; and phosphorylation at STY residues as variable modifications; and 1% False Discovery Rate (FDR). The match between runs option was used to increase the number of trusted IDs. The normalized Intensity values of the Phospho (STY)Sites.txt output was used for the subsequent analysis."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Raw LC–MS/MS files acquired on the LTQ-Orbitrap Velos were processed using MaxQuant version 2.6.7.0. Spectra were searched against the Saccharomyces cerevisiae UniProt reference proteome (strain ATCC 204508/S288c). The first-search and main-search MS1 tolerance was set to 20 ppm, and MS2 tolerance to 0.5 Da. Carbamidomethylation of cysteine was set as a fixed modification; oxidation (M) and phosphorylation on serine, threonine, and tyrosine (STY) were defined as variable modifications. Trypsin/P was specified as the digestion enzyme, allowing up to two missed cleavages. Peptide-spectrum matches, peptides, and proteins were filtered at 1% false discovery rate using a target–decoy approach. The “match between runs” option was enabled to increase identification overlap across replicates. Phosphosite assignments were extracted from the Phospho (STY)Sites.txt output. Further analysis was performed in Perseus (v2.1.3.0). Identifications annotated as contaminants, reverse hits, or with phosphorylation probability below 70% were removed. Intensities were log₂-transformed, and phosphopeptides were required to be quantified in at least two of three biological replicates per condition or present exclusively in one condition. Wild-type W303 control signals were used to remove background binders. Differential phosphorylation analysis between Rrp6- and Rrp46-associated complexes was conducted using Student’s t-test (p ≤ 0.05). Heatmaps and functional enrichment analyses were generated from the filtered dataset to characterize phosphorylation patterns associated with distinct exosome assemblies. To refine the phosphoproteomic dataset toward exosome-related processing, all identified phosphoproteins were first filtered in Perseus annotation tool. Proteins were manually inspected and classified into two categories: (i) candidates involved in rRNA processing and nucleo-cytoplasmic transport, and (ii) all remaining proteins. This classification is provided in the supplementary table 1, where the column “BP” assigns 1 to proteins not associated with these pathways and values 2–10 to proteins grouped into specific rRNA-processing and transport sub-processes. Only the curated candidates (BP = 2–10) were used as input for the Gene Ontology functional analyses. GO terms for Biological Process and Molecular Function were retrieved directly from the Gene Ontology resource and subsequently consolidated into higher-order categories for interpretation."],"omics_type":["Proteomics"],"labhead":["Carla Columbano de Oliveira"],"instrument_platform":[""],"labhead_affiliation":["Department of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000, São Paulo, SP, Brazil."],"submission_type":["PARTIAL"],"species":["Saccharomyces Cerevisiae (baker's Yeast)"],"submitter_mail":["flp_astolpho@uenf.br"],"publication":["10.1021/ACS.JPROTEOME.6C00095"],"submitter_affiliation":["Laboratory of Chemistry and Function of Proteins and Peptides"],"submitter_country":["Brazil"],"additional_accession":[]},"is_claimable":false,"name":"Phosphorylation patterns of pre-ribosomal proteins associated with exosome subunits","description":"This project investigates the phosphorylation landscape of protein factors associated with distinct assemblies of the RNA exosome in Saccharomyces cerevisiae. The RNA exosome is a conserved 3′–5′ exoribonuclease complex essential for pre-rRNA processing, ribosome biogenesis, and RNA quality control. Although its structural organization and cofactors have been well characterized, the regulatory contribution of post-translational modifications, particularly phosphorylation, to exosome recruitment and function remains poorly understood. To address this, we performed comparative phosphoproteomic analyses of protein complexes co-purified with either the nuclear subunit Rrp6 or the core subunit Rrp46. Yeast strains expressing TAP-tagged Rrp6 or Rrp46 were grown in controlled conditions and used for tandem affinity purification (TAP)–based co-immunoprecipitation. A wild-type W303 strain served as a negative control to subtract background interactors. Cell lysates were obtained by cryogenic milling and clarified by ultracentrifugation before incubation with IgG-Sepharose. After TEV protease elution, proteins were lyophilized and subjected to in-solution digestion with sequencing-grade trypsin. Phosphopeptides were enriched using TiO₂ spin tips and analyzed by nano-LC–MS/MS on an LTQ-Orbitrap Velos operated in data-dependent acquisition mode. Raw files were processed with MaxQuant (v2.6.7.0) using standard parameters for phosphosite identification and a 1% FDR cutoff. Across biological triplicates, the dataset comprises 756 phosphorylated peptides and 111 high-confidence phosphosites functionally linked to rRNA maturation, pre-ribosomal particle assembly, nucleocytoplasmic transport, exosome cofactors, and ribosome biogenesis. Principal component analysis confirmed strong replicate clustering. Comparative analysis revealed phosphorylation events exclusive to either Rrp6- or Rrp46-associated complexes, as well as shared sites indicative of constitutive regulatory functions. Several phosphosites mapped to core exosome subunits (Csl4, Rrp4, Rrp6) and cofactors such as Mpp6, Mtr4, and Ski7, highlighting regulatory hotspots potentially involved in exosome recruitment dynamics and cytoplasmic versus nuclear functions. Functional interrogation of selected residues (e.g., Ski7-S90 and Rrp4-S152) demonstrated differential growth phenotypes upon alanine substitution, supporting their biological relevance. Together, these data provide a comprehensive phosphoproteomic profile of exosome-associated assemblies at distinct stages of ribosome maturation. The dataset enables exploration of post-translational regulatory mechanisms governing exosome recruitment, activity modulation, and interaction with ribosomal precursors and cofactors. The high-resolution phosphosite map supplied here offers an important resource for understanding dynamic control of RNA metabolism in eukaryotes and supports future mechanistic studies on exosome regulation and ribosome biogenesis.","dates":{"publication":"2026-08-13","submission":"2026-01-26"},"accession":"PXD073587","cross_references":{"TAXONOMY":["NEWT:68239","NEWT:108018","NEWT:377960","NEWT:1131","NEWT:190486","NEWT:2737160","NEWT:2042546","NEWT:148942","NEWT:193528","NEWT:295546","NEWT:258594","NEWT:1126","NEWT:1129","NEWT:89187","NEWT:309807","NEWT:89184","NEWT:309800","NEWT:57577","NEWT:1150591","NEWT:156563","NEWT:1323429","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:2315688","NEWT:44270","NEWT:592321","NEWT:1073882","NEWT:6819","NEWT:77173","NEWT:93217","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:10034","NEWT:10031","NEWT:82569","NEWT:661410","NEWT:488003","NEWT:224326","NEWT:109376","NEWT:376619","NEWT:3765","NEWT:2433","NEWT:1190602","NEWT:3767","NEWT:433727","NEWT:135622","NEWT:672127","NEWT:656061","NEWT:37965","NEWT:656064","NEWT:3760","NEWT:36630","NEWT:381198","NEWT:1176302","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:44250","NEWT:77151","NEWT:317447","NEWT:5537","NEWT:698761","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:1562698","NEWT:1177","NEWT:11308","NEWT:12637","NEWT:2164133","NEWT:1180","NEWT:2767846","NEWT:1343074","NEWT:314344","NEWT:108061","NEWT:143292","NEWT:2767842","NEWT:314345","NEWT:224308","NEWT:3134131","NEWT:49928","NEWT:160621","NEWT:110368","NCBITaxon:5204","NEWT:1916073","NEWT:1303873","NEWT:305400","NEWT:1310161","NEWT:1230383","NEWT:77133","NCBITaxon:5207","NEWT:160620","NCBITaxon:77643","NEWT:1310165","NEWT:114727","NEWT:5516","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:32224","NEWT:11320","NEWT:33554","NEWT:1410384","NEWT:1310173","NEWT:37919","NEWT:1072569","NEWT:1072568","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:135666","NEWT:419481","NEWT:5507","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:1143","NEWT:1336794","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:709964","NEWT:3710","NEWT:65125","NEWT:3712","NEWT:3711","NEWT:3714","NEWT:65121","NEWT:3716","NEWT:3715","NEWT:2065263","NEWT:1549675","NEWT:177437","NEWT:9014","NEWT:10891","NEWT:118221","NEWT:32201","NEWT:34869","NEWT:226126","NEWT:1616117","NEWT:34865","NEWT:28174","NEWT:550537","NEWT:284812","NEWT:284811","NEWT:980415","NEWT:2902907","NEWT:3701","NEWT:3702","NEWT:66440","NEWT:1245466","NEWT:3704","NEWT:1246791","NEWT:34875","NEWT:10882","NEWT:1431297","NEWT:9005","NEWT:34871","NEWT:9006","NEWT:33548","NEWT:1883426","NEWT:657321","NEWT:1423687","NEWT:657322","NEWT:34878","NEWT:10886","NEWT:3707","NEWT:3708","NEWT:189423","NEWT:536231","NEWT:219813","NEWT:1301262","NEWT:319224","NEWT:2305479","NEWT:215451","NEWT:460519","NEWT:272843","NEWT:272844","NEWT:1348799","NEWT:55784","NEWT:485","NEWT:223074","NEWT:2709072","NEWT:2499525","NEWT:467144","NEWT:142786","NEWT:28196","NEWT:2853422","NEWT:487","NEWT:1679718","NEWT:387344","NEWT:657318","NEWT:480","NEWT:67767","NEWT:46835","NEWT:216778","NEWT:376686","NEWT:237610","EFO:0001352","NEWT:1385720","NEWT:219809","NEWT:219808","NEWT:119562","NEWT:367737","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:141469","NEWT:272831","NEWT:987059","NEWT:491","NEWT:422203","NEWT:460523","NEWT:2422","NEWT:2423","NEWT:3755","NEWT:133894","NEWT:85694","NEWT:85692","NEWT:911045","NEWT:3750","NEWT:123606","NEWT:1195466","NEWT:2483192","NEWT:85698","NEWT:291146","NEWT:29466","NEWT:233271","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:278161","NEWT:415978","NEWT:410289","NEWT:191701","NEWT:9054","NEWT:472","NEWT:29459","NEWT:34839","NEWT:476","NEWT:1380096","NEWT:28128","NEWT:470","NEWT:41122","NEWT:1328300","NEWT:748693","NEWT:106299","NCBITaxon:50557","NEWT:63363","NEWT:3735","NEWT:29491","NEWT:911022","NEWT:446","NEWT:153481","NEWT:714485","NEWT:445","NEWT:427924","NEWT:2003758","NEWT:29486","NEWT:63366","NEWT:64697","NEWT:63367","NEWT:29488","NEWT:215402","NEWT:3726","NEWT:1120755","NEWT:1862567","NEWT:591090","NEWT:30455","NEWT:28141","NEWT:9030","NEWT:9031","NEWT:3728","NEWT:29471","NEWT:108931","NEWT:219799","NEWT:1325292","NEWT:219798","NEWT:548","NEWT:150475","NEWT:546","NEWT:1431340","NEWT:256737","NEWT:51350","NEWT:8694","NEWT:8692","NEWT:542","NEWT:394503","NEWT:13076","NEWT:219785","NEWT:451515","NEWT:8673","NEWT:550","NEWT:10804","NEWT:52694","NEWT:554","NEWT:2642239","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:42410","NEWT:40686","NEWT:1225786","NEWT:366497","NEWT:771870","NEWT:8665","NEWT:51338","NEWT:771875","NEWT:377142","NEWT:9995","NEWT:28112","NEWT:49012","NEWT:28110","NEWT:10832","NEWT:311339","NEWT:507601","NEWT:520","NEWT:64657","NEWT:186441","NEWT:2585209","NEWT:643680","NEWT:214092","NEWT:40697","NEWT:13095","NEWT:162425","NEWT:242124","NEWT:9986","NEWT:8654","NEWT:536","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:595495","NEWT:80833","NEWT:479096","NEWT:28108","NEWT:28104","NEWT:1114957","NEWT:568703","NEWT:568708","NEWT:480020","NEWT:51315","NEWT:52641","NEWT:353152","NEWT:116597","NEW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