Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/protein_expression_profile.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_22.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_26.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_18.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_13.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_21.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_17.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_25.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_20.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_16.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_15.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_9.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_29.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_24.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_30.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_23.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_14.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_28.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_27.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067020/TMT_19.rawprimaryOK2002004chch@hunaas.cnlihua caoMass SpectrometryBottom-up proteomicsBackfat developmentAdipose tissueCarcass traitsProteomicsLipid metabolism.https://www.ebi.ac.uk/pride/archive/projects/PXD067020Adipose TissueA total of 18 Ningxiang pigs (barrows) were selected at six distinct postnatal developmental stages: 60, 120, 180, 240, 300, and 360 days, with three biological replicates per stage. The animals were provided by Hunan Liushahe Ecological Animal Husbandry Co., Ltd. Backfat tissue samples were collected within 30 minutes post-mortem from the thickest point of the shoulder, immediately snap-frozen in liquid nitrogen, and stored at −80 °C until proteomic analysis.Backfat tissues were ground in liquid nitrogen and lysed in SDT buffer (4% SDS, 100 mM Tris-HCl, pH 7.6). The lysate was homogenized, sonicated, and boiled for 15 minutes. After centrifugation at 14,000 × g for 15 minutes, the supernatant was filtered through a 0.22 μm membrane. Protein concentration was determined using the BCA protein assay kit (P0012, Beyotime, China), and protein integrity was assessed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE).For each sample, 200 μg of protein was diluted with 30 μL SDT buffer. Detergents and low-molecular-weight components were removed using UA buffer (8 M urea, 150 mM Tris-HCl, pH 8.5) via ultrafiltration (30 kDa cutoff, Sartorius). The concentrate was alkylated with 100 μL iodoacetamide (100 mM in UA buffer) for 30 minutes in darkness. After additional UA and triethylammonium bicarbonate (TEAB) buffer washes, proteins were digested with 4 μg trypsin in 0.1 M TEAB buffer overnight at 37 °C. The resulting peptides were quantified by OD280 using a NanoDrop 3000 (Thermo Fisher Scientific, USA). Subsequently, 100 μg peptide per sample was labeled with 41 μL of TMT reagent (Thermo Fisher Scientific, USA) for 1 hour at room temperature. The reaction was quenched with 8 μL of 5% hydroxylamine, followed by 15-minute incubation. Labeled peptides were pooled for high-pH reversed-phase chromatography. TMT-labeled peptides were fractionated on a 1260 Infinity II HPLC system (Agilent, USA) using a high-pH reversed-phase (hpRP) gradient. Samples were diluted in buffer A (10 mM ammonium formate, 5% ACN, pH 10.0) and loaded onto a XBridge Peptide BEH C18 column (130 Å, 5 μm, 4.6 mm × 100 mm). Peptides were eluted at 1 mL/min with a gradient from 0–7% buffer B (10 mM ammonium formate, 85% ACN, pH 10.0) over 5 min, 7–40% buffer B from 5–40 min, 40–100% buffer B from 40–45 min, and held at 100% buffer B for 15 min. Absorbance was monitored at 214 nm, and fractions were collected every minute and dried under vacuum at 45 °C. Each fraction was analyzed using an EASY-nLC system (Thermo Fisher Scientific, USA) coupled to a Q Exactive Plus mass spectrometer (Thermo Fisher Scientific, USA). Peptides were separated on an Acclaim PepMap RSLC C18 column (50 μm × 15 cm, P/N 164943) at a flow rate of 300 nL/min. The gradient consisted of: 6% buffer B for 3 min, 6–28% B over 42 min, 28–38% B over 5 min, 38–100% B over 5 min, and hold at 100% B for 5 min. Mass spectrometry (MS) analysis was performed on a Q Exactive Plus mass spectrometer (Thermo Fisher Scientific, USA) at LC Sciences (Hangzhou, Zhejiang, China). The mass spectrometer operated in positive ion mode with the following settings: MS1 scan range: 350–1800 m/z, MS1 resolution: 70,000, AGC target: 3 × 10⁶, Max injection time: 50 ms, MS2 scans: Top 10 data-dependent scans after each MS1, MS2 resolution: 35,000. Isolation window: 2 m/z, Normalized collision energy: 30 eV, Max MS2 injection time: 45 ms.PrideNot availableMS raw data were processed using Proteome Discoverer v2.1 (Thermo Fisher Scientific， USA) and searched using the MASCOT v2.6 engine (Matrix Science, UK). Protein identifiers were mapped to gene symbols using the UniProt ID Mapping service (release 2025_03). Differentially abundant proteins across developmental stages were identified using one-way ANOVA (P < 0.05) with Benjamini-Hochberg FDR correction. Tukey’s HSD post-hoc tests were performed for pairwise comparisons. Data visualization was conducted using ggplot2 (Villanueva and Chen, 2019) and pheatmap (Kolde and Kolde, 2015) in R.Weighted Gene Co-expression Network Analysis (WGCNA) (Langfelder and Horvath, 2008) was used to identify co-abundance modules. Protein data were normalized prior to analysis. The soft-thresholding power (β = 6) was selected based on scale-free topology (R² = 0.8). The adjacency matrix and topological overlap matrix (TOM) were computed, and hierarchical clustering was used to identify modules. Modules with eigengene correlations >0.8 were merged. Module-trait relationships were assessed using pearson correlation with developmental stages and carcass traits from our previously published dataset (Zhang et al., 2024). Modules with |R| > 0.7 and P < 0.05 were considered biologically significant. Significance of these associations was empirically validated through 1000 permutation tests (P<0.05), confirming the non-random nature of the observed correlations and reinforcing the biological validity of the identified co-expression modules. Hub proteins were prioritized based on module membership scores. Gene Ontology (GO) enrichment was conducted using the GO Enrichment Analysis tool (geneontology.org), powered by PANTHER (version 20240807) (Mi et al., 2013), with the GO Ontology database (release 2025-03-16; DOI: 10.5281/zenodo.15066566). Fisher’s exact test with FDR correction (FDR < 0.05) was applied. Protein–protein interaction (PPI) networks were constructed and visualized using igraph and ggraph packages in R.ProteomicsChen ChenPARTIALHunan Institute of Animal and Veterinary ScienceSus Scrofa Domesticus (domestic Pig)42121728 Cao L, Chen Y, Cui Q, Deng Y, Zhu J, Ren H, Hu X, Qiu M, Zhang X, Sun R, Tang Z, Wang H, Peng Y, Chen C. Age-Driven Proteomic Networks in Ningxiang Pig Backfat Identify Candidate Regulators of Carcass Traits. Animals (Basel). 2026 16(9):1309 10.3390/ani16091309caolihua@hunaas.cnHunan Institute of Animal and Veterinary ScienceChinaIndigenous pigs constitute crucial genetic reservoirs. Adipose tissue is central to pig growth and metabolism, yet its molecular ontogeny remains poorly characterized in indigenous breeds such as the Ningxiang pig. We employed mass spectrometry to profile backfat proteomes across six postnatal stages (60-360 days). Proteomes clearly separated early (60-120 days) from late stages (300-360 days). Older pigs showed enrichment in processes linked to energy metabolism, translation, immune function, and mitochondrial activity. We identified 43 lipid metabolism proteins exhibiting significant age-dependent abundance. Weighted co-abundance network analysis revealed four protein modules significantly correlated with lean meat percentage, fat percentage, and carcass weight. Intramodular analysis identified four hub proteins-ALDH18A1, FABP4, FBP1, and HADHB-as putative candidates associated with lipid transport, gluconeogenesis, and fatty acid oxidation. This study links temporal proteomic profiles with key carcass traits, providing a data resource and a network-based framework for future research.Age-Driven Proteomic Networks in Ningxiang Pig Backfat Identify Candidate Regulators of Carcass Traits.Cao Lihua L, Chen Yu Y, Cui Qingming Q, Deng Yuan Y, Zhu Ji J, Ren Huibo H, Hu Xionggui X, Qiu Meizhen M, Zhang Xing X, Sun Rongguang R, Tang Zhiqiang Z, Wang Huiming H, Peng Yinglin Y, Chen Chen CfalseProteomic profiling reveals age-dependent remodeling of backfat and key regulatory proteins linked to carcass traits in ningxiang pigsAdipose tissue plays a critical role in growth, energy metabolism, and carcass composition in pigs. However, the age-dependent molecular mechanisms underlying backfat development remain poorly characterized, particularly in native breeds such as the Ningxiang pig, which exhibits high fat deposition and distinct growth patterns. This study aimed to characterize the dynamic proteomic changes in backfat tissue across postnatal development and identify molecular pathways and candidate proteins associated with economically important carcass traits. We performed a comprehensive proteomic analysis of backfat tissue collected from Ningxiang pigs across seven postnatal developmental stages (day 60 to 360). Using high-resolution mass spectrometry, we quantified dynamic changes in protein abundance and explored their functional relevance through gene ontology (GO) enrichment and network-based analyses. Principal component analysis revealed clear age-related separation in proteomic profiles, particularly between early (day 60–120) and later developmental stages. GO enrichment analysis of differentially abundant proteins indicated significant overrepresentation of biological processes related to energy metabolism, translation, immune response, and mitochondrial function in older age groups. Further curation of lipid metabolism pathways identified hundreds of proteins involved in lipogenesis and lipolysis, many of which displayed distinct age-dependent expression patterns. To link protein expression to economically important traits, we performed weighted gene co-expression network analysis (WGCNA), identifying four protein modules significantly associated with carcass characteristics such as lean meat percentage, fat content, and carcass weight. From these modules, we identified four key hub proteins— ALDH18A1, FABP4, FBP1, and HADHB—with known roles in lipid transport, gluconeogenesis, amino acid metabolism, and fatty acid oxidation, respectively. This study provides novel insights into the proteomic remodeling of backfat during postnatal development and highlights potential molecular targets for improving carcass quality in pigs. Our findings contribute to a deeper understanding of adipose tissue biology and offer a valuable resource for future genetic and breeding strategies.This study provides the first in-depth proteomic characterization of backfat development across seven postnatal stages in Ningxiang pigs, a native Chinese breed known for high fat deposition. By integrating high-resolution mass spectrometry with gene ontology and co-expression network analyses, we uncovered dynamic, age-dependent changes in protein abundance linked to key biological processes, including energy metabolism, immune function, and mitochondrial activity. Notably, we identified four protein modules significantly associated with carcass traits such as lean meat percentage and fat content, and highlighted four hub proteins (ALDH18A1, FABP4, FBP1, and HADHB) as potential molecular markers for selective breeding. These findings advance our understanding of adipose tissue biology and provide actionable molecular targets for improving carcass composition in pigs. The work also offers a valuable reference dataset for future functional genomics and precision breeding efforts in indigenous and commercial pig populations.2026-06-082025-08-07PXD067020NEWT:330879NEWT:377960NEWT:2042546NEWT:259447NEWT:295546NCBITaxon:2719036NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:59753NEWT:89184NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:1073882NEWT:475174NEWT:1117NEWT:498257NEWT:10036NEWT:1590NEWT:10034NEWT:661410NEWT:638632NEWT:224326NEWT:376619NCBITaxon:79857NEWT:1096976NEWT:1589NEWT:135622NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:656064NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:641809NEWT:38815NEWT:317447NEWT:4688NEWT:7719NEWT:868565NEWT:135674NEWT:79329NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:224308NEWT:3347NEWT:160621NEWT:212790NEWT:110368NEWT:1310161NEWT:77133NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:44688NEWT:44689NEWT:498211NEWT:347256NEWT:5518NEWT:398007NEWT:1527468NEWT:498217NEWT:498216NEWT:11320NEWT:246196NEWT:246197NEWT:145458NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:3329NEWT:419481NEWT:5507NEWT:410661NEWT:1140NCBITaxon:2157NEWT:1143NEWT:1287689NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:1182590NEWT:3712NEWT:3711NEWT:270643NEWT:2065263NEWT:177437NEWT:10418NEWT:118698NEWT:1616117NEWT:118696NEWT:34865NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:44664NEWT:43346NEWT:3702NEWT:1245466NEWT:244366NEWT:1246791NEWT:118694NEWT:2850NEWT:118691NEWT:34871NEWT:33548NEWT:52299NEWT:8165NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:460519NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:1303443NEWT:9483NEWT:485NEWT:56636NEWT:2853422NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:1185650NEWT:216778NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:1883446NEWT:1233435NEWT:109760NEWT:29031NEWT:317047NEWT:460523NEWT:235443NEWT:1757312NEWT:85694NEWT:108458NEWT:5936NEWT:320637NEWT:1078283NEWT:3750NEWT:983964NEWT:11706NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:3747NEWT:1116234NEWT:1255228NEWT:410289NEWT:373153NEWT:472NEWT:940825NEWT:529507NEWT:1071661NEWT:470NEWT:5911NCBITaxon:50557NEWT:39251NEWT:29491NEWT:101841NEWT:446NEWT:153481NEWT:2014887NEWT:33952NEWT:445NEWT:153009NEWT:261756NEWT:166313NEWT:63366NEWT:63367NEWT:215402NEWT:1547NEWT:906914NEWT:9031NEWT:27292NEWT:1050722NEWT:108931NEWT:1293497NEWT:1055524NEWT:150475NEWT:267872NEWT:381666NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:8694NEWT:33936NEWT:8692NEWT:2903NEWT:185579NEWT:13076NEWT:1006581NEWT:8673NEWT:33940NEWT:550NEWT:554NEWT:451516NEWT:552NEWT:1325291NEWT:36185NEWT:1054211NEWT:1225786NEWT:51338NEWT:575412NEWT:28112NEWT:6493NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:9986NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:9983NEWT:8655NEWT:5147NEWT:28108NEWT:28104NEWT:407821NEWT:568703NCBITaxon:2NEWT:568708NEWT:986NEWT:52641NEWT:28532NEWT:353152NEWT:298176NEWT:40674NEWT:1194669NEWT:51329NEWT:443906NEWT:519NEWT:2510939NEWT:7394NEWT:6063NEWT:1328388NEWT:1548728NEWT:667127NEWT:9557NEWT:377586NEWT:300641NEWT:39655NEWT:9554NEWT:38323NEWT:475932NEWT:256318NEWT:206411NCBITaxon:6191NEWT:229533NEWT:214053NEWT:80863NEWT:90675NEWT:52638NEWT:57075NEWT:1666905NEWT:8697NEWT:8695NEWT:884204NEWT:1123869NEWT:9544NEWT:9545NEWT:979NEWT:7370NEWT:83906NEWT:99488NEWT:1134506NEWT:255470NEWT:38783NEWT:6426NEWT:33090NEWT:9935NEWT:287889NEWT:305959NEWT:13489NEWT:29829NEWT:92867NEWT:92866NCBITaxon:3055NEWT:51750NEWT:202950NEWT:295027NCBITaxon:11320NEWT:632957NEWT:9925NCBITaxon:9606NEWT:90690NEWT:1436183NEWT:300273NEWT:4232NEWT:416348NEWT:11298NEWT:4236NEWT:7742NEWT:196627NEWT:200308NEWT:200302NEWT:870435NEWT:9913NEWT:9915NEWT:105841NEWT:2666255NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:9909NEWT:9902NEWT:430615NEWT:72664NEWT:563041NEWT:36599NEWT:41949NEWT:249161NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1678078NEWT:749906NEWT:418985NEWT:749907NEWT:150847NEWT:29835NEWT:431947NEWT:69014NEWT:142809NEWT:302409NEWT:130821NEWT:27606NEWT:1519788NEWT:59202NEWT:9975NEWT:8643NEWT:1159899NEWT:502780NEWT:860688NEWT:13443NEWT:35231NEWT:8644NEWT:1125630NEWT:5141NEWT:46360NCBITaxon:3044782NEWT:202914NEWT:160235NEWT:502779NEWT:297246NEWT:8639NEWT:1928434NEWT:8637NEWT:1114970NEWT:2096NEWT:192222NEWT:9963NEWT:1617910NEWT:637379NEWT:2785785NEWT:411901NEWT:1298722NEWT:8626NEWT:186801NEWT:105884NCBITaxon:9615NEWT:8621NEWT:58334NEWT:58331NEWT:8624NEWT:5116NEWT:8623NEWT:5597NCBITaxon:3077NEWT:194439NCBITaxon:12637NEWT:38727NEWT:218496NEWT:8618NEWT:70448NEWT:300251NEWT:9940NEWT:1247190NEWT:118702NEWT:118700NEWT:2126719NEWT:118705NEWT:6945NEWT:2104NEWT:2627626NEWT:6943NEWT:157546NEWT:870726NEWT:91374NEWT:91373NEWT:474186NEWT:54195NEWT:10136NEWT:38942NEWT:4762NEWT:6941NEWT:307972NEWT:2102NEWT:34NEWT:38949NEWT:1299114NEWT:1590841NEWT:1276473NEWT:2282334NEWT:1247NEWT:70667NEWT:869728NEWT:6938NCBITaxon:39054NEWT:1736309NEWT:4751NEWT:1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