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DaSilva"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Lc-ms","Heat-stress","Proteomics","Pollen","Tomato"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD053410"],"tissue":["Plant Cell","Pollen"],"sample_protocol":["tomato Pollen Sample lysates were transferred to the custody of the Proteomics Core Facility in approximately 200L of 5% SDS and 8M Urea pH 7.5 buffer. Samples were diluted to 100g in Lysis Buffer (5% Sodium Dodecyl Sulfate (SDS, Invitrogen, 15553-035) in 50mM Triethylammonium Bicarbonate (TEAB, Sigma Aldrich, T7408-100ML)) for proteomic profiling. Samples were subjected to S-Trap Micro Digestion and Clean-up (Protifi, C02-micro-40) as specified by the manufacturer with some modifications. Samples were reduced using 11L of Dithiothreitol (DTT, 10mM final concentration, Sigma Aldrich, 646563-10X.5ML) and incubated at 55C for 45 minutes with mixing. Following incubation, samples were alkylated using 12L of Iodoacetamide (IAM, 20mM final concentration, Thermo Scientific, A39271) and incubated at room temperature in the dark for 30 minutes. Following alkylation, samples were acidified using 30L of Phosphoric Acid (2.5% final concentration, Sigma Aldrich, 79617-250ML), and vortexed for 30 seconds. 900L of ice-cold Binding Buffer (9 parts LC/MS Grade Methanol (ACROS Organics, 61513-0025):1 part 1M TEAB (100mM Final concentration)) was added to each sample before the entire sample was transferred to each S-Trap spin column and centrifuged for 30 seconds at 4000xg. Each sample was then washed once with 150L of binding buffer. Following protein washing, 1 vial (20g) of Trypsin (Promega, V5111) was reconstituted in 50mM TEAB and added to each micro spin column to yield a final concentration of 1g of trypsin for 20g of protein in 100L. Samples were then moved to a humidified chamber in a 37C incubator and left overnight (18hrs).   On Day 2, samples were left to cool to room temperature for 15 minutes before 40L of 50mM TEAB was added and each sample was centrifuged for 1 minute at 4000xg. Peptides were eluted with 40L of LC/MS grade Water (Honeywell, 39253-4X2.5L) and 0.1% Formic Acid (Fisher Scientific, A117-50), and centrifuged again for 1 minute at 4000xg. Finally, to completely elute hydrophobic peptides, 40L of 50% LC/MS Grade Acetonitrile (Fisher, A955-4) was added to each sample and allowed to stand for 5 minutes before being centrifuged for 1 minute at 4000xg. Each sample was concentrated using a speed vacuum concentrator (Thermo Fisher Scientific) for approximately 90 minutes. With solvent removed, samples were reconstituted in 100uL of Solvent A (Water with 0.1% Formic Acid) and spiked with indexed retention time peptides (Biognosys, Ki-3002-1) in a 1:50 dilution to monitor HPLC performance.Samples were then injected onto a QExactive Orbitrap LC/MS system (Thermo Fisher Scientific) and separated over a 120-minute gradient consisting of solvent A (water + 0.1% Formic Acid), and solvent B (Acetonitrile and 0.1% Formic Acid) using a split-flow set-up on an Agilent 1200 series HPLC system. A 15cm long (75um ID) capillary analytical column packed with XSelect CSH C18 2.5 μm resin (Waters) from the University of Arkansas for Medical Sciences (UAMS) National Proteomic Resource Center (NPRC) was used to separate digested peptides. The 120-minute gradient consisted of 95% Solvent A for 1 minute, 70% solvent A for 94 minutes, 5% solvent A for 6 minutes and finally 100% solvent A for the remaining 20 minutes all at a flow rate of 0.240 ml/min. The mass spectrometer acquisition utilized a Full MS/ddMS2 (Top9) centroid experiment. Full MS parameters used a default charge state of 2, 1 microscan, resolution of 70,000, AGC target of 3e6, 200ms Maximum Injection time, in a scan range of 400-1800m/z. ddMS2 parameters were 1 microscan, resolution of 17,500, AGC target of 2e4, a max injection time of 200ms, a loop count of 9, Top 9 precursors, Isolation window of 2.5m/z, collision energy of 28, and a scan range of 200-2000 m/z. Data dependent settings consisted of a minimum AGC target of 2e2, 1e3 intensity threshold, unassigned charge exclusion, all charge states, preferred peptide match, isotope exclusion, 30 seconds of dynamic exclusion."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":[".raw files were processed using MaxQuant (Ver 2.1.4.0) using 1% peptide and protein FDR search constraints, all values were default except for 20ppm first search tolerance and 7 ppm main search tolerance against the latest version of the Heinz Tomato protein .fasta file. Variable modifications consisted of just oxidation (M) and protein N-terminal Acetylation. Carbamidomethylation was the sole static modification for the Trypsin/P search. Match between runs algorithm was unselected and intensity-based absolute quantification (iBAQ) was selected. The proteingroups.txt file output was further processed in excel and Relative IBAQ was calculated as the intensity of each protein divided by the sum of all intensities for each given sample. DEqMS/ RStudio was also used to generate DEPs."],"omics_type":["Proteomics"],"labhead":["Mark Johnson"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Brown University  Department of Molecular Biology, Cellular Biology, and Biochemistry"],"species":["Solanum Lycopersicum"],"publication":["10.1073/PNAS.2611706123"],"submitter_mail":["nicholas_dasilva@brown.edu"],"submitter_affiliation":["Brown University\nDirector, Proteomics Core Facility \nDeptartments of Molecular Biology, Cell Biology, and Biochemistry"],"submitter_country":["United States"],"additional_accession":[]},"is_claimable":false,"name":"Pollen tube integrity is critical for thermotolerance in tomato and is enhanced by loss of SlRALF1","description":"Heat stress occurs when temperatures exceed ideal growth conditions, posing a major threat to plant reproduction by affecting male developmental processes such as pollen formation and function. This critical biological process involves complex events from gamete formation and pollination to fruit and seed development. Among essential crops, cultivated tomato (Solanum lycopersicum) is vital for global food security. Elevated temperatures during the reproductive stages can disrupt pollen viability, fertilization, and fruit set, leading to reduced production and quality. Therefore, selecting tomato cultivars with varying degrees of thermal tolerance is crucial in a changing climate. in our study, we will explore one thermosensitive cultivars (Heinz (Hz), and two thermotolerant cultivars  Nagcarlang (Ng) and Tamaulipas (Tm) to determine the strategies used by pollen tube of thermotolerant cultivars to improve pollen performance during pollen tube initiation and early elongation at higher temperatures.","dates":{"publication":"2026-10-01","submission":"2024-06-26"},"accession":"PXD053410","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:330879","NEWT:35554","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:295546","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:1129","NEWT:309807","NEWT:55153","NEWT:10244","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:638632","NEWT:263737","NEWT:224326","NEWT:1333499","NCBITaxon:79857","NEWT:1096976","NEWT:5702","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:96731","NEWT:383379","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:3112","NEWT:4442","NEWT:31155","NEWT:192875","NEWT:1214915","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:108061","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:931281","NEWT:4432","NEWT:658457","NEWT:1310161","NEWT:77133","NEWT:295358","NEWT:145481","NCBITaxon:79824","NEWT:2246","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:44447","NEWT:752555","NEWT:498211","NEWT:5759","NEWT:1736231","NEWT:5518","NEWT:398007","NEWT:1392","NEWT:498217","NEWT:498216","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:1367269","NEWT:633149","NEWT:10239","NEWT:44685","NEWT:161934","NEWT:4897","NEWT:1148","NEWT:5508","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:4896","NEWT:1287689","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1336795","NEWT:644042","NEWT:294","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:3711","NEWT:935293","NEWT:375146","NEWT:2065263","NEWT:118698","NEWT:1616117","NEWT:263","NEWT:118696","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:3702","NEWT:243277","NEWT:7067","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:33548","NEWT:274","NEWT:408172","NEWT:408170","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:1436733","NEWT:460519","NEWT:1247411","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:9483","NEWT:333760","NEWT:1513458","NEWT:1233681","NCBITaxon:40559","NEWT:506599","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NCBITaxon:4932","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:2719099","NEWT:983964","NEWT:118499","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:3983","NEWT:352472","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:2014887","NEWT:33952","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:272634","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:141262","NEWT:108931","NEWT:1055524","NEWT:4087","NEWT:9778","NEWT:306","NEWT:150475","NEWT:303","NEWT:267872","NEWT:7111","NEWT:347515","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:4090","NEWT:4092","NEWT:9541","NEWT:8694","NEWT:4093","NEWT:4096","NEWT:8692","NEWT:185579","NEWT:941442","NEWT:13076","NEWT:1226408","NEWT:7108","NEWT:40479","NEWT:43989","NEWT:4076","NEWT:317","NEWT:1006581","NEWT:885318","NEWT:39488","NEWT:550","NEWT:4081","NEWT:273068","NEWT:554","NEWT:98334","NEWT:451516","NEWT:4084","NEWT:63577","NEWT:36185","NEWT:1225786","NEWT:7574","NEWT:1715256","NEWT:30640","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:28112","NEWT:114155","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:6239","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8655","NEWT:1263854","NEWT:118503","NEWT:2059687","NEWT:160488","NEWT:28104","NEWT:207559","NEWT:407821","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:986","NEWT:52641","NEWT:7159","NEWT:28532","NEWT:198618","NEWT:353152","NEWT:8496","NEWT:27448","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:243230","NEWT:1080772","NEWT:519","NEWT:8479","NEWT:8485","NEWT:6063","NEWT:49240","NEWT:104395","NEWT:6289","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:469008","NEWT:256318","NEWT:9321","NEWT:206411","NCBITaxon:6191","NEWT:596153","NEWT:229533","NEWT:1836","NEWT:2925","NEWT:214053","NEWT:80863","NEWT:105231","NEWT:74649","NEWT:52638","NEWT:57075","NEWT:4097","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:9785","NEWT:627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