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For each replicate, approximately 100 mg of fresh tissue was flash-frozen in liquid nitrogen and ground into a fine powder. Protein extraction was performed using a trichloroacetic acid (TCA)/acetone precipitation protocol. Briefly, powdered samples were homogenized in 4 mL of extraction buffer containing 10% (w/v) trichloroacetic acid (TCA) and 0.07% (v/v) dithiothreitol (DTT) in cold acetone. Homogenates were mixed thoroughly and stored overnight at –20 °C. centrifuged at 10,000 × g for 1 h at 4 °C, and supernatants were discarded. Pellets were washed twice with 4 mL of cold rinse solution (0.07% v/v DTT in acetone). After each wash, samples were incubated at –20 °C for 1 h, centrifuged at 10,000 × g for 30 min at 4 °C, and supernatants were discarded. Final pellets were air-dried under a laminar flow hood for 10 min. Dried pellets were resuspended in 1 mL of solubilization buffer containing 8 M urea and 50 mM triethylammonium bicarbonate (TEAB), pH 8.5, supplemented with protease inhibitors (1 mM phenylmethylsulfonyl fluoride, PMSF, and protease inhibitor cocktail; Sigma-Aldrich). Samples were vortexed and incubated overnight at 30 °C under gentle agitation. Following incubation, samples were centrifuged at 12,000 × g for 5 min at 4 °C, and supernatants were collected. Protein reduction was performed by adding 100 µL of 100 mM DTT to each sample and incubating at 60 °C for 1 h. Alkylation was carried out by adding 300 µL of 120 mM iodoacetamide (IAM) and incubating the sample for 1 h at room temperature in the dark. Proteins were subsequently precipitated by adding cold acetone at a 5:1 (v/v) ratio and incubating overnight at –20 °C. Samples were centrifuged at 12,000 × g for 5 min at 4 °C, and supernatants were discarded. Protein concentration was determined using the Bio-Rad Protein Assay (Bio-Rad, Hercules, CA, USA) according to the manufacturer’s instructions. For enzymatic digestion, 100 µg of protein from each sample was digested with sequencing-grade trypsin (2 µL, 1 mg/mL) and incubated overnight at 37 °C. Digestion was stopped by cooling the samples on ice for 10 min. The resulting peptide mixtures were dried, resuspended in 50 µL of 50% (v/v) acetonitrile (ACN) containing 0.1% (v/v) trifluoroacetic acid (TFA), and desalted using ZipTip™ C18 pipette tips prior to LC–MS/MS analysis.PrideNot availableLabel-free proteomic analysis was performed with three 3 technical replicates on the selected samples using a Thermo Scientific Orbitrap Exploris 240 mass spectrometer coupled online to an UltiMate 3000 RSLC nano-HPLC system (Dionex, Sunnyvale, CA, USA) via a Nanoflex ion source (Thermo Fisher Scientific). Peptides were loaded onto an Acclaim PepMapTM RSLC C18 column (150 mm × 75 μm ID, 2 μm particles, 100 Å pore size) (Thermo-Fisher Scientific) and separated at flow rate was 300 nL/min using a binary solvent system consisting of solvent A (water with 0.1% v/v formic acid) and solvent B (acetonitrile/water/formic acid, 80/19.92/0.08 v/v/v) in 1 min. The column was held at 97% solvent B for 8 min and then returned to 3% solvent B in 1 min, followed by a re-equilibration period of 20 min.ProteomicsSimonetta CairaCNR-ISPAAMPARTIALBrassica Napus (rape)42125617 Ertani A, Esposito M, Caira S, Riahi J, Colombani C, Scaloni A, Paradiso R, Bulgari R. Blue-enriched LED light modulates biochemical and proteomic traits without affecting yield in indoor-grown cress microgreens. Front Plant Sci. 2026 17:1814329 10.3389/fpls.2026.1814329simonetta.caira@cnr.itConsiglio Nazionale delle RicercheItalyLight spectral composition is a key driver of plant growth and quality in controlled-environment agriculture. This study evaluated the effects of two LED light spectra differing in blue, green, red, and far-red proportions on growth, nutritional traits, and proteomic profiles of indoor-grown cress (Lepidium sativum L.) microgreens. Plants were cultivated under two B:G:R:FR ratios (13:15:61:11 and 24:12:56:8) at identical photosynthetic photon flux density (255 μmol m-2 s-1). Growth parameters, including plantlet height, fresh and dry weight, dry matter percentage, and yield, did not differ significantly between treatments. Similarly, nitrate content, total chlorophylls, total carbon, total nitrogen, and the C/N ratio remained unchanged. In contrast, the blue-enriched and far-red-reduced spectrum significantly enhanced secondary metabolite accumulation, increasing anthocyanin concentration and phenolic index rising by 77% and 52%, respectively. Microgreen proteomics revealed a general plant reprogramming depending on LED light irradiation, mostly involving components associated with photosynthesis, protein physical control/biosynthesis/homeostasis/modification, multi-process regulation, RNA biosynthesis, vesicle trafficking, redox homeostasis or with unknown function, which showed over- or down-represented trends according to their nature. Notably, these molecular adjustments occurred without compromising growth or productivity. Overall, these results demonstrate that targeted manipulation of LED light quality can enhance the functional and nutritional quality of microgreens through proteomic reprogramming while maintaining yield, highlighting light spectrum modulation as a promising strategy for sustainable indoor and vertical farming systems. Repository data: PRIDE accession number PXD077094 (ProteomeXchange).Blue-enriched LED light modulates biochemical and proteomic traits without affecting yield in indoor-grown cress microgreens.Ertani Andrea A, Esposito Mariapia M, Caira Simonetta S, Riahi Jouhaina J, Colombani Carla C, Scaloni Andrea A, Paradiso Roberta R, Bulgari Roberta RfalseBlue-enriched LED light modulates biochemical and proteomic traits without affecting yield in indoor-grown cress microgreensLight spectral composition is a key driver of plant growth and quality in controlled-environment agriculture. This study evaluated the effects of two LED light spectra differing in blue, green, red, and far-red proportions on growth, nutritional traits, and proteomic profiles of indoor-grown cress (Lepidium sativum L.) microgreens. Plants were cultivated under two B:G:R:FR ratios (13:15:61:11 and 24:12:56:8) at identical photosynthetic photon flux density (255 μmol m⁻² s⁻¹). Growth parameters, including plantlet height, fresh and dry weight, dry matter percentage, and yield, did not differ significantly between treatments. Similarly, nitrate content, total chlorophylls, total carbon, total nitrogen, and the C/N ratio remained unchanged. In contrast, the blue-enriched and far-red-reduced spectrum significantly enhanced secondary metabolite accumulation, increasing anthocyanin concentration and phenolic index rising by 77% and 52%, respectively. Microgreen proteomics revealed a general plant reprogramming depending on LED light irradiation, mostly involving components associated with photosynthesis, protein physical control/biosynthesis/homeostasis/modification, multi-process regulation, RNA biosynthesis, vesicle trafficking, redox homeostasis or with unknown function, which showed over-or down-represented trends according to their nature. Notably, these molecular adjustments occurred without compromising growth or productivity. Overall, these results demonstrate that targeted manipulation of LED light quality can enhance the functional and nutritional quality of microgreens through proteomic reprogramming while maintaining yield, highlighting light spectrum modulation as a promising strategy for sustainable indoor and vertical farming systems.2026-05-182026-04-13PXD077094NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:10245NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:43186NEWT:428146NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:661410NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:383379NEWT:1401257NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:1214915NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:5763NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NEWT:2652724NEWT:5757NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:145458NEWT:633149NEWT:1149786NEWT:10239NEWT:68895NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5744NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1235816NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:2065263NEWT:1772NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:11988NEWT:284812NEWT:8175NEWT:400667NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:459758NEWT:3702NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:7070NCBITaxon:287NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:1436733NEWT:460519NEWT:1247411NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:333760NEWT:56636NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:81077NEWT:84588NEWT:1679718NEWT:480NEWT:65349NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:109760NEWT:943274NEWT:644223NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:1130798NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:1218097NCBITaxon:50557NEWT:39251NEWT:39491NCBITaxon:5811NEWT:29491NEWT:101841NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:688333NEWT:215402NCBITaxon:548681NEWT:318586NEWT:272634NEWT:198107NEWT:9031NEWT:1872122NEWT:1308NEWT:7091NEWT:1034015NEWT:760568NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:97477NEWT:7111NEWT:347515NEWT:172269NEWT:9534NEWT:6269NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:536088NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT:142615NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:208893NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:5147NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:353152NEWT:8496NEWT:7165NEWT:27448NEWT:40674NEWT:1194669NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:104395NEWT:9557NEWT:6289NEWT:377586NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:9554NEWT:118562NEWT:725NEWT:7137NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:90675NEWT:105231NEWT:104385NEWT:74649NEWT:52638NEWT:57075NEWT:206672NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:9793NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:27457NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:419610NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NCBITaxon:102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