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Homogenization was done using PreOmics BeatBox magnetic beads for 10 min, then samples were heated at 95°C for 10 min. For BONCAT analysis, lysates were alkylated with 100 μL of 600 mM chloroacetamide (CAA) in 0.8% SDS/PBS (65°C, 30 min, dark). Alkylated lysates were mixed with 600 μL of 8 M urea/0.85 M NaCl in PBS and 30 or 40 μL DBCO-agarose beads. Copper-free click reactions proceeded for 24 h at room temperature in the dark. After removing supernatants, beads were reduced in 500 μL of 5 mM DTT in 0.8% SDS/PBS (70°C, 15 min, 1200 RPM, dark) and alkylated again with 500 μL of 40 mM CAA (30 min, dark). Beads were washed sequentially with 50 mL 0.8% SDS in PBS, 50 mL urea/Tris-HCl (pH 8.0), and 50 mL 20% ACN in water. On-bead digestion occurred overnight at 37°C with 0.1 μg trypsin and 0.05 μg LysC. Peptides were collected using Pierce™ Centrifuge Columns after centrifugation (1 min, 1.5k RCF). Samples were desalted (PreOmics Phoenix Kit), dried, and reconstituted in 10 μL 0.2% formic acid (FA) for LC-MS/MS analysis. For whole lysate proteomics, 50 µg protein of lysate underwent digestion using an S-Trap micro spin column according to manufacturer's instructions. Eluted peptides were desalted using Pierce™ C18 spin columns, dried, and resuspended in 2% ACN, 0.2% FA for LC-MS/MS. Peptides were analyzed on an Eclipse mass spectrometer coupled to a Vanquish Neo UHPLC system. Peptides from BONCAT-enriched samples were separated on an Aurora UHPLC Column (25 cm x 75 µm, 1.7 µm C18, AUR3-25075C18-TS, Ion Opticks) with a flow rate of 0.35 µL/min for a total duration of 1 h and ionized at 1.6 kV in the positive ion mode. The gradient was composed of 6% solvent B (3.5 min), 6-25% B (41.5 min), 25-40% B (15 min), 40–98% B (2 min) and 98% B (5min), with the remaining volume composed of solvent A, where solvent A is 2% ACN and 0.2% FA in water, and solvent B is 80% ACN and 0.2% formic acid in water. For samples from whole lysates, 2 µg of peptides were separated on an Aurora Frontier™ column (60 cm × 75 μm, 1.7 μm C18, AUR3-60075C18, Ion Opticks) at 0.30 µL/min for a total duration of 2 h and ionized at 1.8 kV. The gradient was composed of 6% solvent B (7.5 min), 6-25% B (82.5 min), 25-40% B (30 min), 40–98% B (1 min) and 98% B (9 min). MS1 scans were acquired in the Orbitrap at the resolution of 120,000 from 375 to 1,600 m/z. Automatic gain control (AGC) was set to a target of 106 and a maximum injection time of 50 ms. MS2 scans were acquired in the ion trap using fast scan rate on precursors with 2-7 charge states and quadrupole isolation mode (isolation window: 1.2 m/z) with higher-energy collisional dissociation (HCD, 30%) activation type. Dynamic exclusion was set to 30 s. Ion transfer tube temperature was 300°C and the S-lens RF level was set to 30.PrideMS raw files were searched against the Uniprot Danio rerio proteome (UP000000437) using the Proteome Discoverer 3.0 software based on the SequestHT algorithm. Oxidation / +15.995 Da (M), deamidated / +0.984 Da (N) were set as dynamic modifications; carbamidomethylation / +57.021 Da (C) was set as a fixed modification. The precursor mass tolerance was set to 10 ppm; fragment mass tolerance was set to 0.6 Da. The maximum false peptide discovery rate was specified as 0.01 using the Percolator Node validated by q-value. The relative abundance of parental peptides was calculated by integration of the area under the curve of the MS1 peaks using the Minora LFQ node.ProteomicsTsui-Fen ChouProteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, United StatesPARTIALDanio Rerio (zebrafish) (brachydanio Rerio)41980224 Miller SE, Wang TY, Quan B, Cammidge T, Chou TF, Prober DA, Tirrell DA. Time-Resolved Proteomic Analysis in Zebrafish Using Bioorthogonal Noncanonical Amino Acid Tagging. J Proteome Res. 2026 25(5):2263-2278 10.1021/acs.jproteome.5c00845tywang@caltech.eduCaltechUnited StatesTracking time-dependent proteomic changes remains challenging. Bioorthogonal noncanonical amino acid tagging (BONCAT) offers a targeted approach for identifying proteins synthesized within defined time windows. Here, we describe BONCAT proteomic analysis in larval zebrafish, a model organism widely used for its genetic tractability and utility in developmental biology and neuroscience. We enriched and identified azidohomoalanine-labeled proteins via mass spectrometry after labeling durations as short as 12 h, achieving significant signal above background compared to unlabeled controls. As a proof of concept, we investigated proteomic changes in response to heat shock. BONCAT analysis revealed upregulation of heat shock-induced proteins with greater sensitivity than global proteomics. Gene set enrichment analysis confirmed that heat shock response proteins were significantly enriched in BONCAT samples but not in whole lysates, highlighting BONCAT's ability to detect otherwise-masked transient molecular responses. Beyond the expected changes in synthesis of heat shock proteins, BONCAT identified differentially expressed proteins implicated in stress responses, lipid metabolism, and neural regulation, offering insights into the zebrafish heat shock response. These findings establish BONCAT as a powerful tool for time-resolved proteomic analysis in zebrafish, and for elucidation of the molecular underpinnings of behavior, stress responses, and development in this versatile model organism.Time-Resolved Proteomic Analysis in Zebrafish Using Bioorthogonal Noncanonical Amino Acid Tagging.Miller Sophie E SE, Wang Ting-Yu TY, Quan Baiyi B, Cammidge Tasha T, Chou Tsui-Fen TF, Prober David A DA, Tirrell David A DAfalseTime-resolved proteomic analysis in zebrafish larvae using bioorthogonal noncanonical amino acid tagging (BONCAT)Protein synthesis underpins many biological processes, yet tracking time-dependent proteomic changes remains challenging. Bioorthogonal noncanonical amino acid tagging (BONCAT) offers a targeted approach for labeling and identifying newly synthesized proteins within defined time windows of interest. Here, we present the first such application of BONCAT in larval zebrafish, a model organism that has seen widespread use because of its genetic tractability and utility in developmental biology and neuroscience. We successfully enriched, using click chemistry, and identified, via mass spectrometry, azidohomoalanine (AHA)-labeled proteins after labeling durations as short as 12 hours. Proteomic analysis of BONCAT-enriched proteins demonstrated significant signal above background compared to unlabeled controls after both 48 h and 12 h of labeling. As a proof of concept, we investigated proteomic changes in response to heat shock in zebrafish larvae. BONCAT analysis revealed the upregulation of heat shock-induced proteins with greater sensitivity than whole lysate proteomics. Gene set enrichment analysis confirmed that known heat shock response proteins were significantly enriched in the BONCAT dataset but not in the whole lysate dataset, highlighting the ability of BONCAT to detect transient molecular responses otherwise masked in conventional whole lysate approaches. Beyond the expected changes in synthesis of heat shock proteins, BONCAT identified differentially expressed proteins implicated in stress responses, lipid metabolism, and neural regulation, offering insights into the zebrafish heat shock response. These findings establish BONCAT as a powerful tool for time-resolved proteomic analysis in zebrafish. Its ability to enhance signal specificity and resolve protein dynamics opens new avenues for studying molecular underpinnings of behavior, stress, and development in this versatile model organism.2026-06-082025-04-18PXD063084NEWT:330879NEWT:377960NEWT:2042546NEWT:259447NEWT:295546NCBITaxon:2719036NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:59753NEWT:89184NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:1117NEWT:498257NEWT:10036NEWT:1590NEWT:661410NEWT:638632NEWT:224326NEWT:376619NCBITaxon:79857NEWT:1096976NEWT:1589NEWT:135622NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:641809NEWT:317447NEWT:4688NEWT:7719NEWT:868565NEWT:135674NEWT:79329NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:224308NEWT:3347NEWT:160621NEWT:212790NEWT:1310161NEWT:77133NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:44688NEWT:44689NEWT:498211NEWT:347256NEWT:5518NEWT:398007NEWT:1527468NEWT:498217NEWT:498216NEWT:11320NEWT:246196NEWT:246197NEWT:145458NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:3329NEWT: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:3702NEWT:1245466NEWT:244366NEWT:1246791NEWT:118694NEWT:2850NEWT:118691NEWT:34871NEWT:33548NEWT: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:1502NEWT:128017NEWT:376686NEWT:95486NEWT:1883446NEWT:1233435NEWT:109760NEWT:29031NEWT:235443NEWT:108458NEWT:5936NEWT:320637NEWT:3750NEWT:983964NEWT:11706NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:3747NEWT:1116234NEWT:1255228NEWT:410289NEWT:373153NEWT:472NEWT:529507NEWT:1071661NEWT:470NEWT:5911NCBITaxon:50557NEWT:39251NEWT:29491NEWT:101841NEWT:446NEWT:153481NEWT:2014887NEWT:33952NEWT:445NEWT:153009NEWT:261756NEWT:63366NEWT:63367NEWT:215402NEWT:1547NEWT:9031NEWT:27292NEWT:1050722NEWT:108931NEWT:1293497NEWT:1055524NEWT:150475NEWT:267872NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:8694NEWT:33936NEWT:8692NEWT:2903NEWT:185579NEWT:13076NEWT:1006581NEWT:8673NEWT:33940NEWT:550NEWT:554NEWT:451516NEWT:552NEWT:1325291NEWT:36185NEWT:1054211NEWT:1225786NEWT:575412NEWT:28112NEWT:6493NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:9986NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:8655NEWT:5147NEWT:28104NEWT:407821NCBITaxon:2NEWT:568708NEWT:986NEWT:52641NEWT:28532NEWT:353152NEWT:40674NEWT:1194669NEWT:51329NEWT:443906NEWT:519NEWT:2510939NEWT:6063NEWT:1328388NEWT:1548728NEWT:667127NEWT:9557NEWT:377586NEWT:300641NEWT:39655NEWT:9554NEWT:38323NEWT:256318NEWT:206411NCBITaxon:6191NEWT:229533NEWT:214053NEWT:80863NEWT:90675NEWT:52638NEWT:57075NEWT:8697NEWT:8695NEWT:884204NEWT:1123869NEWT:9544NEWT:9545NEWT:979NEWT:7370NEWT:83906NEWT:1134506NEWT:255470NEWT:38783NEWT:6426NEWT:33090NEWT:9935NEWT:287889NEWT:305959NEWT:13489NEWT:92867NEWT:92866NCBITaxon:3055NEWT:51750NEWT:202950NEWT:295027NCBITaxon:11320NEWT:632957NEWT:9925NCBITaxon:9606NEWT:90690NEWT:1436183NEWT:4232NEWT:416348NEWT:11298NEWT:196627NEWT:200308NEWT:200302NEWT:870435NEWT:9913NEWT:9915NEWT:105841NEWT:2666255NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:430615NEWT:72664NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1678078NEWT:749906NEWT:418985NEWT:749907NEWT:150847NEWT:431947NEWT:69014NEWT:142809NEWT:302409NEWT:130821NEWT:27606NEWT:1519788NEWT:59202NEWT:9975NEWT:8643NEWT:1159899NEWT:502780NEWT:860688NEWT:13443NEWT:8644NEWT:5141NEWT:46360NCBITaxon:3044782NEWT:202914NEWT:160235NEWT:502779NEWT:297246NEWT:8639NEWT:1928434NEWT:8637NEWT:1114970NEWT:2096NEWT:192222NEWT:9963NEWT:1617910NEWT:2785785NEWT:411901NEWT:1298722NEWT:8626NEWT:105884NCBITaxon:9615NEWT:8621NEWT:58334NEWT:58331NEWT:8624NEWT:5116NEWT:8623NEWT:5597NCBITaxon:3077NEWT:194439NCBITaxon:12637NEWT:38727NEWT:8618NEWT:70448NEWT:9940NEWT:1247190NEWT:118702NEWT:118700NEWT:2126719NEWT:118705NEWT:6945NEWT:2104NEWT:2627626NEWT:6943NEWT:157546NEWT:870726NEWT:91374NEWT:91373NEWT:474186NEWT:10136NEWT:38942NEWT:4762NEWT:307972NEWT:2102NEWT:34NEWT:38949NEWT:1299114NEWT:1590841NEWT:1276473NEWT:2282334NEWT:1247NEWT:70667NEWT:869728NEWT:6938NCBITaxon:39054NEWT:1736309NEWT:4751NEWT:194963NEWT:15819NEWT:109461NEWT:1085956NEWT:6928NEWT:1239NEWT:36745NEWT:400727NEWT:272563NEWT:11009NEWT:3885NEWT:3888NEWT:649408NEWT:6915NEWT:101510NEWT:3880NEWT:272559NEWT:216816NEWT:153151NEWT:515849NEWT:10141NEWT:95767NEWT:466585NEWT:1000589NEWT:85963NEWT:29NEWT:85962NEWT:42197NEWT:143361NEWT:1299NEWT:424718NEWT:316407NEWT:1794699NCBITaxon:183674NEWT:167387NEWT:84645NEWT:1123294NEWT:209285NEWT:211586NEWT:747078NEWT:1282NEWT:1283NEWT:1000561NEWT:2133NEWT:294381NEWT:197NEWT:1390363NEWT:35889NEWT:406072NEWT:29176N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