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Ariel IsernData-dependent acquisitionMass SpectrometryBottom-up proteomicsChagas DiseaseSerine hydrolasesChagas diseaseActivity-based protein profilingFluorophosphonate probesTrypanosoma cruzihttps://www.ebi.ac.uk/pride/archive/projects/PXD080813Cell CultureTrypanosoma cruzi Dm28c epimastigotes were maintained at mid-log phase in LIT medium (5 g/L liver infusion broth, 5 g/L bacto-tryptose, 68 mM NaCl, 5.3 mM KCl, 22 mM Na₂HPO₄, 0.4% (w/v) glucose, pH 7.4) supplemented with 5 µM hemin and 10% fetal bovine serum (FBS) at 28 °C. For activity-based protein profiling, 1.5 × 10⁸ epimastigotes (5 × 10⁷ cells/mL) were incubated with the indicated activity-based probes (10 µM) for 30 min at 28 °C. Cells were collected by centrifugation (3,500 × g, 5 min, 4 °C), washed three times with ice-cold PBS, and lysed in 25 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1% Triton X-100, and 5% glycerol supplemented with EDTA-free protease inhibitor cocktail. Lysates were clarified by centrifugation (13,000 × g, 10 min, 4 °C), and protein concentrations were determined using a BCA assay. For CuAAC, clarified lysates (2 mg/mL) were reacted with biotin-azide (50 µM), CuSO₄ (1 mM), TBTA (0.1 mM), and sodium ascorbate (1 mM) for 1 h at room temperature. Proteins were precipitated by addition of nine volumes of ice-cold methanol, incubated overnight at −80 °C, pelleted (10,000 × g, 10 min, 4 °C), washed twice with ice-cold methanol, air-dried, resuspended in 2% SDS/PBS, and diluted to 0.1% SDS. Biotinylated proteins were enriched using pre-washed NeutrAvidin-agarose beads (50 µL/sample) for 2 h at room temperature with end-over-end rotation. Beads were sequentially washed three times with 0.5% SDS/PBS, three times with 6 M urea/PBS, three times with PBS, and once with 50 mM triethylammonium bicarbonate (TEAB). On-bead proteins were reduced with 10 mM TCEP (45 min, 30 °C), alkylated with 15 mM α-iodoacetamide (45 min, dark, room temperature), and digested overnight at 37 °C in 100 mM TEAB using sequencing-grade modified trypsin (4 µg/sample). Peptides were collected, beads were washed twice with 50% acetonitrile containing 0.1% formic acid, wash fractions were combined with the digest, acidified to pH 3 with formic acid, vacuum-dried, desalted using Pierce Peptide Desalting Spin Columns according to the manufacturer's instructions, and dried again before LC-MS analysis. Peptides were separated on an Ultimate 3000 nanoHPLC coupled to a Q Exactive HF Orbitrap mass spectrometer using an EASY-Spray PepMap RSLC C18 column (50 cm × 50 µm ID) at 300 nL/min with 0.1% formic acid in water (A) and acetonitrile (B). A linear gradient of 4–30% B over 114 min, 30–80% B over 14 min, and 80% B for 2 min was employed. MS data were acquired in positive ion mode using data-dependent acquisition with full MS scans (m/z 375–2,000, resolution 120,000, AGC 1 × 10⁶, maximum injection time 100 ms), followed by MS/MS of the eight most intense precursor ions (normalized collision energy 28, resolution 30,000, AGC 5 × 10⁵, isolation window 1.4 m/z, maximum injection time 55 ms). Singly charged, unassigned, and ≥7 charged ions were excluded, and a dynamic exclusion of 30 s was applied.PrideNot availableAll raw LC-MS/MS data were processed using FragPipe (v22.0).1 Protein identification was carried out using MSFragger (v4.1),2 and label-free quantification was performed using IonQuant (v1.10.27).3 Searches were performed as two independent FragPipe runs, each against a separate T. cruzi Dm28c genome assembly (2018 and 2014). The following search parameters were used: trypsin digestion with maximum 2 missed cleavages, carbamidomethylation of cysteine as a fixed modification, oxidation of methionine, acetylation of protein N-termini as variable modifications, minimum peptide length of 7, a maximum number of modifications per peptide set at 3, and protein false discovery rate (FDR) 0.01. All subsequent data processing and statistical analysis were performed in R (v4.5.0), using scripts adapted by the authors from open-source scripts by Richter and Isern et al. (https://doi.org/10.1038/s41467-026-73804-8). 4 LFQ intensity values were log2-transformed to normalize distribution. Data distribution and variability were assessed using density plots (ggplot2),5 boxplots, and mean-standard deviation plots (IceR). Missing data were imputed using a left-censored normal distribution approach, akin to the Perseus strategy.6 Specifically, missing values were replaced with random values drawn from a normal distribution shifted 1.8 standard deviations below the mean and scaled by a factor of 0.3. The quality of the imputation was assessed via replicate correlation plots and distributional comparisons before and after imputation. Differential abundance analysis was conducted using the limma package.7 A linear model was fitted for each protein across the two conditions (e.g., “Probe” vs. “Ctrl”), empirical Bayes moderation was applied to the variance estimates. Proteins were considered differentially abundant based on a dual threshold of |log2(fold change)| > 1 and p-value < 0.05. Although Benjamini–Hochberg false discovery rate (FDR)-adjusted p-values were computed, nominal p-values were used for thresholding given the target-discovery nature of this workflow, so as not to discard genuine low-abundance targets; candidate hits were subsequently prioritized by manual curation. Protein identifiers were cleaned and standardized to ensure uniqueness prior to analysis. Each run was analysed separately, and the serine hydrolases identified as enriched across the two assembly searches were combined into a single set of candidate targets. Significant protein abundance changes were visualized using EnhancedVolcano (version 1.14.0).ProteomicsPatrick G. SteelPARTIALDepartment of Chemistry, Durham University, Stockton Rd, DH1 3LE, Durham, United KingdomTrypanosoma Cruzi Dm28c10.64898/2026.07.18.739127jaime.a.isern@gmail.comDurham UniversityUnited KingdomfalseFunctional Mapping of the Trypanosoma cruzi Serinome by Fluorophosphonate Activity-Based Protein ProfilingSerine hydrolases (SHs) constitute one of the largest enzyme superfamilies in eukaryotes, yet their roles in Trypanosoma cruzi, the causative agent of Chagas disease, remain largely uncharacterized. Here, we report an activity-based chemoproteomic map of the T. cruzi epimastigote serinome by combining genome-informed in silico curation with whole-cell activity-based protein profiling (ABPP) using a panel of cell-permeable fluorophosphonate (FP)-alkyne probes. Whole-cell labelling followed by label-free quantitative proteomics (LFQ-MS), identified 37 enriched SH-like proteins, including 35 with conserved or partially conserved catalytic triad/dyad features, spanning lipases, peptidases, esterases, and previously uncharacterized hydrolases. The 35 SHs represent approximately 63 % of the 56 predicted SHs retained after catalytic-site curation. Domain architecture analysis revealed broad structural diversity, while orthologue-based localization data suggested association with multiple subcellular compartments, including glycosomal, mitochondrial, and endosomal localizations. Gene Ontology enrichment highlighted lipid metabolic and catabolic processes as dominant functional themes, and protein–protein interaction network analysis supported functional connectivity among the captured enzymes. Several identified SHs, including oligopeptidase B, prolyl oligopeptidase Tc80, serine carboxypeptidase CPB1, and phospholipase A1 (PLA1) have previously been characterized in trypanosomatids as virulence factors and as mediator of host-pathogen interactions. Together, these findings establish a fluorophosphonate-based chemoproteomic resource for the kinetoplastid community and prioritize probe-accessible active T. cruzi SHs for future functional validation and antiparasitic inhibitor discovery.2026-07-212026-07-09PXD080813NEWT: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:1912919NEWT:5757NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:1367269NEWT: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: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: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:552NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT: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:51329NEWT: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:413071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