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Samples were collected on the last SD and then after 2, 4 and 7 days under LD conditions (2LD, 4LD and 7LD). Five to six biological replicates were collected for each time point. Each biological replicate corresponded to leaves coming from 16 plants (4 leaves per plant; total 64 leaves). Phloem sap from each biological replicate was collected in 4 individual low-binding 0.5 ml eppendorf tubes with 0.5 ml ml Milli-Q water with protease inhibitor (0.2 mM phenylmethylsulfonyl fluoride (PMSF)). Exudation of phloem content was allowed for 8 hours, placing the tubes places in a dark humid chamber during this time. Samples were adjusted to 1 % sodium deoxycholate (SDC), 10 mM DL-dithiothreitol and 50 mM ammonium bicarbonate (AmBic) and heated to 95 °C for 15 min. Then, they were alkylated by adding 0.2 M iodoacetamide solution and incubating for 30 min at room temperature (RT) in the dark. Samples were then concentrated on a 10 KDA filter (Millipore) by centrifugation by 10000 rpm, now containing big proteins (Fraction A). The eluate from the 10 KDA filter contained mainly small proteins/peptides (Fraction C). Both fractions, A and C, were digested by adding 1 μg of trypsin (Promega/SDS Biosciences) in 50 mM AmBIc and 1% SDC and incubating overnight (~16 h) at 37°C. After adding trifluoroacetic acid (TFA) to a final concentration of 0.5 % w/v to stop the reaction and precipitate SDC, samples were centrifuged at 14000 g and the supernatants were cleaned using C-18 tips on 96-well plates (Waters and BioTage). The resulting peptides were eluted with 0.1 % TFA in 65 % acetonitrile (ACN). The eluates were then evaporated to dryness and stored at −80 °C until preparation for analysis by adding glycogen phosphorylase (50 fmol/μl) dissolved in 0.1 % TFA. 3 to 5 µl of each sample was loaded on a BEH C18 analytical column (75 μm internal diameter × 250 mm, 1.7 μm particles; Waters, MA, USA), and separated using a concave 68.5 min gradient of 1–40% solvent B (0.1% formic acid in acetonitrile) in solvent A (0.1% aqueous formic acid) at a flow rate of 300 nl min–1. The eluate was passed to a nano-electrospray ionization-equipped SynaptTM G2-Si HDMS mass spectrometer (Waters, MA, USA) operating in a resolution mode. All data were collected both using run in MSE with dynamic range extension enabled using a scan time of 0.4 s, mass-corrected using Glu-fibrinopeptide B and Leu-enkephalin as reference peptidesPrideNot availableThe data from the MSE run were processed with Progenesis QI v2.0 (Nonlinear Dynamics Ltd.,Waters, Newcastle, UK). The resulting spectra were searched against the Arabidopsis thaliana databases Araport 11 and small open reading frames ORFs (ARA-PEP; ATSO).The database search settings for MSE run were: enzyme-specific cleavage with one miscleavage allowed; carbamidomethylated cysteines as fixed modification; oxidized methionine, N-terminal acetylation, deamidated asparagine, O-GlcNAcylation (ST) and Phosphorylation (STY) as variable modifications. A minimum of three fragments were required for a peptide detection with a precursor and fragment tolerance of 15 and 25 ppm, respectively with a false discovery rate <4%. 7 fragments were needed for a protein identification.ProteomicsReyes Benlloch OrtizPlant Biology Department Faculty of Pharmacy University of ValenciaPARTIALArabidopsis Thaliana (mouse-ear Cress)41937606 Moreno-Sanguino I, Collás LA, Samuelsson G, Wingsle G, Benlloch R. Phloem Proteomics to Identify Small Open Reading Frame (sORF)-encoded Peptides With a Putative Role in the Control of Flowering Time in Arabidopsis. Physiol Plant. 2026 178(2):e70860 10.1111/ppl.70860reyes.benlloch-ortiz@uv.esDepartment of Plant Biology. Faculty of Pharmacy and Food Sciences. Univeristy of Valencia.SpainPhloem sap proteomic studies have previously revealed that phloem sap composition varies during development and upon floral induction. Specific proteins, lipids, messenger RNAs (mRNAs), and peptides have been shown to accumulate at different developmental stages. Peptides are of special interest since they have the potential to act as regulatory molecules controlling plant responses to environmental changes, such as salinity and water stress, plant-microbe interactions, and developmental changes. In this context, we have characterized Arabidopsis thaliana phloem exudates to identify proteins and peptides with the potential to control flowering time, acting as signals fine-tuning plant development. In this work, we present the proteomic profiles of the phloem sap samples during floral transition along with the identification of proteins and peptides that showed changes in abundance during floral transition, suggesting that they could potentially have a role in the control of flowering. Among those, we have described the abundance pattern of the sORF1511 peptide in the phloem sap, which varies upon floral induction. We show that sORF1511 overexpression affects bolting time and alters the expression of several genes involved in the control of flowering time.Phloem Proteomics to Identify Small Open Reading Frame (sORF)-encoded Peptides With a Putative Role in the Control of Flowering Time in Arabidopsis.Moreno-Sanguino Irene I, Collás Lucía Argente LA, Samuelsson Göran G, Wingsle Gunnar G, Benlloch Reyes RfalsePhloem proteomics in Arabidopsis thaliana: identification of small peptidesThe objective of this study is to analyse the protein composition of A. thaliana phloem at different stages of development. For this purpose phloem exudates have been collected at different time points (vegetative stage, floral transition and reproductive stage).2026-04-132025-06-23PXD065325NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:43186NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:96731NEWT:383379NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:1214915NEWT:12637NEWT:59729NEWT:2164133NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NEWT:2652724NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:633149NEWT:10239NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT: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:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:7070NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1436733NEWT:460519NEWT:1247411NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:333760NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:84588NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:109760NEWT:943274NEWT:644223NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:39491NCBITaxon:5811NEWT:29491NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:215402NCBITaxon:548681NEWT:272634NEWT:9031NEWT:1872122NEWT:7091NEWT:1034015NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:7111NEWT:347515NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT: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:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:353152NEWT:8496NEWT:7165NEWT:27448NEWT:40674NEWT:1194669NEWT:51329NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:104395NEWT:9557NEWT:6289NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:90675NEWT:105231NEWT:74649NEWT:52638NEWT:57075NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NCBITaxon:10239NCBITaxon:714NEWT:295027NEWT:632957NEWT:11051NEWT:9925NEWT:89462NCBITaxon:9606NEWT:8839NEWT:90690NEWT:1436183NEWT:4232NEWT:2758385NEWT:11298NEWT:171101NEWT:714NEWT:5322NEWT:421932NEWT:312017NEWT:196627NEWT:200308NEWT:553470NEWT:200302NEWT:870435NEWT:284593NEWT:100392NEWT:5315NEWT:9913NEWT:265872NEWT:105841NEWT:337330NEWT:2666255NEWT:2285NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:981087NEWT:180066NEWT:226900NEWT:231490NEWT:244704NEWT:7725NEWT:430615NEWT:563041NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1416333NEWT:35024NEWT:1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