{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/20250716_PC1482-Dohlman_S2_S.cerevisiae_Report_PC_protein_Report_Pivot.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/20250716_PC1482-Dohlman_S2_S.cerevisiae_ConditionSetup.tsv"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/20250716_PC1482-Dohlman_S2_S.cerevisiae_ExperimentSetupOverview_directDIA.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/20250612_Astral_IO-25cm_PC1482-Dohlman_DIA_5.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/20250612_Astral_IO-25cm_PC1482-Dohlman_DIA_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/20250612_Astral_IO-25cm_PC1482-Dohlman_DIA_Pool_R1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/20250612_Astral_IO-25cm_PC1482-Dohlman_DIA_8.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/20250612_Astral_IO-25cm_PC1482-Dohlman_DIA_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/20250612_Astral_IO-25cm_PC1482-Dohlman_DIA_4.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/20250612_Astral_IO-25cm_PC1482-Dohlman_DIA_6.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/20250612_Astral_IO-25cm_PC1482-Dohlman_DIA_Pool_R2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/20250612_Astral_IO-25cm_PC1482-Dohlman_DIA_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/20250612_Astral_IO-25cm_PC1482-Dohlman_DIA_7.raw"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/Uniprot-SCerevisiae_Rev_May2024_tax559292_6727.fasta","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/PC1482_Dohlman_Tpk_Sequences.fasta","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD067402/contaminants_mq1.6_headersForSpectronaut.fasta"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["hdohlman@med.unc.edu"],"submitter":["Scott Lyons"],"technology_type":["Mass Spectrometry","Data-independent acquisition"],"software":[""],"submitter_keywords":["Paralogs","proteomics","bioid","pka","Paralogs; glucose sensing; pka; protein-protein interaction; bioid; proteomics","protein-protein interaction","glucose sensing"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD067402"],"sample_protocol":["Sample Preparation for Affinity Purification Mass Spectrometry Analysis (AP-MS): Protein samples were subjected to on-bead trypsin digestion, as previously described (https://pubmed.ncbi.nlm.nih.gov/33649150/ ). After the last wash buffer step, 50 µl of 50 mM ammonium bicarbonate (pH 8) containing 1 µg trypsin (Promega) was added to beads overnight at 37ºC with shaking. The next day, 500 ng of trypsin was added then incubated for an additional 3 h at 37ºC with shaking. Supernatants from pelleted beads were transferred, then beads were washed twice with 100 μL LC/MS grade water. These rinses were combined with the original supernatant, then acidified using 6 ul of 10% trifluoracetic acid. Peptides were desalted with peptide desalting spin columns (Thermo) and dried via vacuum centrifugation. Peptide samples were stored at -80˚C until further analysis. LC/MS/MS Analysis: Samples were analyzed in a randomized order by LC-MS/MS using a Vanquish Neo coupled to an Orbitrap Astral mass spectrometer (Thermo Scientific). A pooled sample was analyzed three times throughout the sample set. Samples were injected onto an IonOptics Aurora series 2 C18 column (75 μm id × 15 cm, 1.6 μm particle size) (IonOpticks) and separated over a 30 min method. The gradient for separation consisted of 2-30% mobile phase B at a 300 nl/min flow rate, where mobile phase A was 0.1% formic acid in water and mobile phase B consisted of 0.1% formic acid in 80% ACN. Astral was operated in product ion scan mode for Data Independent Acquisition (DIA). A full MS scan (m/z 380-980) was collected; resolution was set to 240,000 with a maximum injection time of 5 ms and AGC target of 500%. Following the full MS scan, a product ion scan was collected (30,000 resolution) and consisted of stepped higher collision dissociation (HCD) set to 25; AGC target set to 500%; maximum injection time set to 55 ms; variable precursor isolation windows 380-980 m/z; the isolation window was set to 3 m/z."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Raw data files were processed using the directDIA method in Spectronaut (v20; Biognosys) and searched against the Uniprot reviewed S.cerevisiae database (ATCC 204508/S288c, containing 6,727 entries, downloaded May 2024) the MaxQuant common contaminants database (246 entries), and human recombinant Tpk1, Tpk2, and Tpk3 fused to TurboID. The following settings were used: enzyme specificity set to trypsin, up to two missed cleavages allowed, methionine oxidation, and N-terminal acetylation set as variable modifications. A false discovery rate (FDR) of 1% was used to filter all data. Cross-run normalization was enabled, imputation was disabled. Imputation and statistical analysis were performed in Perseus software (version 1.6.14.0). Proteins with log2 fold change ≥ 1 and a p-value < 0.05 are considered significant."],"omics_type":["Proteomics"],"labhead":["Henrik Dohlman"],"instrument_platform":[""],"labhead_affiliation":["Department of Pharmacology, University of North Carolina at Chapel Hill"],"submission_type":["PARTIAL"],"species":["Saccharomyces Cerevisiae (baker's Yeast)"],"publication":["41400924 Si Y, Adhikari K, Herring LE, Isom DG, Li S, Lyons SP, McRitchie SL, Rushing BR, Sumner SJ, Dohlman HG. Nonredundant roles for paralogous proteins in the yeast glucose-sensing pathway. Mol Biol Cell. 2026 37(2):ar15 10.1091/mbc.e25-10-0475"],"submitter_mail":["scott_lyons@med.unc.edu"],"submitter_affiliation":["UNC Chapel Hill"],"submitter_country":["United States"],"pubmed_abstract":["Paralogs engage in biological processes through both redundant and nonredundant functions. In the yeast <i>Saccharomyces cerevisiae</i>, approximately one-fifth of the genome consists of paralogs, with their encoded proteins involved in multiple pathways. However, the unique contributions of individual paralogs have remained poorly defined. Here, we undertook a systematic examination of eight paralog pairs in the glucose-sensing pathways, deleting each component and measuring the resulting changes in gene expression. To that end, we established a new transcription reporter system to monitor the response to glucose as well as to nonpreferred sugars in single cells. Focusing on the PKA catalytic subunits, comprised of the paralogs Tpk1 and Tpk3 as well as the isomorphic kinase Tpk2, we employed mass spectrometry to identify their contribution to cellular metabolism, used a GFP-based sensor to follow changes in cytosolic pH, and used BioID to identify unique and shared candidate binding partners. Our data reveal that paralogs in the glucose-sensing pathway contribute in multiple and unique ways to signal transduction, and establish potential mechanisms driving the preservation of these and other duplicated genes throughout long periods of evolution."],"pubmed_title":["Nonredundant roles for paralogous proteins in the yeast glucose-sensing pathway."],"pubmed_authors":["Si Yibo Y, Adhikari Kshitiz K, Herring Laura E LE, Isom Daniel G DG, Li Shuang S, Lyons Scott P SP, McRitchie Susan L SL, Rushing Blake R BR, Sumner Susan J SJ, Dohlman Henrik G HG"],"additional_accession":[]},"is_claimable":false,"name":"Protein-protein interaction network mapping for yeast PKA catalytic subunits using BioID","description":"Paralogs engage in biological processes through both redundant and non-redundant functions. In yeast Saccharomyces cerevisiae, approximately one-fifth of the genome consists of paralogs, with their encoded proteins involved in multiple crucial pathways. However, the contributions of individual paralogs have remained poorly defined. Here, we undertook a systematic examination of eight paralog pairs in the glucose-sensing pathway, including identifying protein-protein interactions (PPIs) through proteomic study. Focusing on the PKA catalytic subunits, comprised of the paralogs Tpk1 and Tpk3 as well as the isomorphic kinase Tpk2, we employed BioID to identify unique and shared binding partners. Our data reveal that, through different PPIs, paralogs in the glucose-sensing pathway contribute in multiple and unique ways to signal transduction, and establish potential mechanisms driving the preservation of these and other duplicated 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