Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/1914-BSFoverexpression-uninduced_control_replicate2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/1847-PCFRNAi-uninduced_control-replicate2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/1922-BSFRNAi-induced_replicate1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/1922-BSFRNAi-uninduced_control-replicate2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/1914-BSFoverexpression-induced_replicate2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/1922-BSFRNAi-induced_replicate2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/1914-BSFoverexpression-uninduced_control_replicate1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/1847-PCFRNAi-uninduced_control-replicate1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/1922-BSFRNAi-uninduced_control-replicate1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/1847-PCFRNAi-induced_replicate2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/1847-PCFRNAi-induced_replicate1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/1914-BSFoverexpression-induced_replicate1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/TriTrypDB-64_TbruceiTREU927_AnnotatedProteins.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/1914-BSFoverexpression.sneftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/1922-BSFRNAi.sneftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075464/PCFRNAi_1847.sneprimaryOK200zoltnerm@natur.cuni.czMartin ZoltnerMass SpectrometryData-independent acquisitionTrypanosomiasisTrypanosoma buceiEndoplasmic reticulumErqchttps://www.ebi.ac.uk/pride/archive/projects/PXD075464Permanent Cell Line CellCell CultureTetracycline inducible RNAi cell lines in T. brucei BSF and PCF, were generated using the pRPaiSL (PMID: 1858891) or the p3666 (PMID: 22511983) based stem-loop RNAi system, respectively, using primers predicted by RNAit2 (PMID: 12706807). Tb927.5.1160 inducible expression in T. brucei BSF relied on the plasmid construct pRPaTag and its integration into the tetracycline-responsive RRNA promoter of 2T1 cells (PMID: 16182389). PCF or BSF cells were induced with tetracyclin (1 g/ml) for Tb927.5.1160 RNAi depletion or overexpression and incubated for 48 h in parallel with nontreated cells. Cultures were harvested within their logarithmic growth phase and 5 x 107 cells resuspended in PBS containing Complete Mini Protease Inhibitor Mixture (Roche), then washed twice in PBS. Samples were then mixed with 100mM TEAB (Triethylammonium bicarbonate) containing 2% SDC (sodium deoxycholate) and lysed by boiling at 95°C for 5 min and sonication (Bandelin Sonoplus Mini 20, MS 1.5). Protein concentration was determined using BCA protein assay kit (Sigma Aldrich). 20 µg of protein was adjusted with 100mM TEAB (Triethylammonium bicarbonate) containing 2% SDC (sodium deoxycholate) to a final concentration of 50 µl, mixed with 40 mM chloroacetamide, 10mM TCEP (Tris(2-carboxyethyl)phosphine) and boiled again. Samples were then mixed with 5 µl of SP3 beads (PMID: 30464214) and 65 µl of 100 % ethanol. After binding, the beads were washed twice with 80% ethanol. The mixture was digested in 100 mM TEAB with 0.5 µg of trypsin overnight at 37°C. After digestion, samples were acidified with TFA to 1% final concentration and peptides were desalted using in-house made stage tips packed with C18 disks (Empore). Nano Reversed phase columns (Ion Opticks, Aurora Ultimate TS 25×75 C18 UHPLC column) were used for LC/MS analysis. LC was performed on a Vanquish NEO UHPLC system (Thermo Scientific). Mobile phase buffer A was composed of water and 0.1% formic acid. Mobile phase B was composed of acetonitrile and 0.1% formic acid. Samples were loaded onto the trap column (C18 PepMap100, 5 μm particle size, 300 μm x 5 mm, Thermo Scientific) in loading buffer composed of water and 0.1% formic acid. Peptides were eluted with a Mobile phase B gradient from 2% to 35% B in 9.6 min. Eluting peptide cations were converted to gas-phase ions by electrospray ionization and analyzed on a Thermo Orbitrap Astral (Thermo Scientific) by data independent approach. Survey scans of peptide precursors from 380 to 980 m/z were performed in orbitrap at 120K resolution (at 200 m/z) with a 5 × 106 ion count target. DIA scans were performed in astral analyzer. AGC target was set to 5 × 104 and maximum injection time to 2 ms. Precursor mass range 380 – 980 m/z was covered by 4 m/z windows. Activation type was set to HCD with 25 % collision energy. Sample layout: (1)Tb927.5.1160 RNAi in PCF T. brucei 2 induced samples and 2 uninduced controls (Experiment 1847) (2)Tb927.5.1160 over-expression in BSF T. brucei 2 induced samples and 2 uninduced controls (Experiment 1914) (3)Tb927.5.1160 RNAi in BCF T. brucei 2 induced samples and 2 uninduced controls (Experiment 1922)PrideNot availableAll data were analyzed and quantified with the Spectronaut 19 software (PMID: 25724911) using directDIA analysis. A spectral library was generated based on the predicted protein sequences for T. brucei TREU927 sourced from TriTrypDB (version 64) (PMID: 36656904). Enzyme specificity was set as C-terminal to Arg and Lys, also allowing cleavage at proline bonds and a maximum of two missed cleavages. Carbamidomethylation of cysteines was set as fixed modification and N- terminal protein acetylation and methionine oxidation as variable modifications. FDR was set to 1 % for PSM, peptide and protein. Quantification was performed on MS2 level. Precursor PEP cutoff and precursor and protein cutoff was set to 0.01, protein PEP was set to 0.05.ProteomicsMartin ZoltherDepartment of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Prague, Czech RepublicPARTIALTrypanosoma Bruceim.zoltner@dundee.ac.ukNot availableDivision of Biological Chemistry & Drug Discovery School of Life Sciences University of Dundee Dundee DD1 5EHUnited KingdomfalseA novel player in trypanosome endoplasmic reticulum quality control with apparent similarities to the mammalian BiP nucleotide exchange inhibitor MANFWe have identified the saponin-domain containing protein Tb927.5.1160 as a novel endoplasmic reticulum (ER) factor in Trypanosoma brucei. Tb927.5.1160 acts proximal to the prototypic ER chaperon BiP, the conserved heat shock protein 70 family chaperon playing a key role in protein folding and ER quality control, and exhibits a conserved BiP binding region shared with the mammalian BiP nucleotide exchange inhibitor MANF (mesencephalic astrocyte-derived neurotrophic factor). We demonstrated by inducible RNAi depletion and over-expression that Tb927.5.1160 has a marked effect on the sensitivity toward ER-stress and is essential for T. brucei viability. Here we deposit whole cell proteomics data monitoring protein abundance changes after 48 hours induction of Tb927.5.1160 RNAi in bloodstream form (BSF) and procyclic-form (PCF) T. brucei, and Tb927.5.1160 overexpression in BSF.2026-04-052026-03-10PXD075464NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:190802NEWT:35554NEWT:9778NEWT:150475NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:307972NEWT:32046NEWT:544496NEWT:5180NEWT:256737NEWT:2042546NEWT:115104NEWT:1081927NEWT:67825NEWT:185579NEWT:43179NEWT:13076NEWT:1249668NEWT:317NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:415540NEWT:4081NEWT:876138NEWT:554NEWT:98334NEWT:426428NEWT:237561NEWT:6928NEWT:10036NEWT:7574NEWT:1351NEWT:7215NEWT:29204NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:3885NEWT:746360NEWT:6239NEWT:3888NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:3641NEWT:383379NEWT:8782NEWT:1263854NEWT:1000589NEWT:1902NEWT:85962NEWT:160488NEWT:28104NEWT:317447NEWT:7955NCBITaxon:2NEWT:985076NEWT:7959NEWT:2261NEWT:4565NEWT:1264690NEWT:6192NEWT:28532NCBITaxon:38727NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:216595NEWT:243230NEWT:8355NEWT:1283NEWT:931281NEWT:1000561NEWT:7029NEWT:1283300NEWT:6183NEWT:6063NEWT:334747NEWT:61235NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:725NEWT:360106NEWT:260707NEWT:287NEWT:10117NEWT:10239NCBITaxon:6191NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:83334NEWT:185431NEWT:83332NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:44685NEWT:2697049NEWT:1148NEWT:11676NEWT:55571NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:1123869NEWT:7370NEWT:75058NEWT:83906NEWT:607699NEWT:6282NEWT:1094343NEWT:208964NEWT:1134506NEWT:575584NEWT:296543NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:1182590NEWT:8726NEWT:6669NEWT:10090NEWT:935293NEWT:64152NEWT:749200NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:990346NEWT:5334NEWT:145953NEWT:257309NEWT:100816NEWT:230741NEWT:284812NCBITaxon:10359NCBITaxon:1313NEWT:43330NEWT:242619NEWT:44544NEWT:632957NEWT:373995NEWT:5689NEWT:645463NEWT:544404NEWT:3702NEWT:129249NEWT:9925NEWT:8839NEWT:4232NEWT:990119NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:421932NEWT:196627NEWT:408172NEWT:5691NEWT:408170NEWT:493760NEWT:260710NEWT:627025NEWT:400772NEWT:1097677NEWT:3708NEWT:128161NEWT:106592NEWT:1117957NEWT:9913NEWT:1432138NEWT:10312NEWT:1424507NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:8030NEWT:29722NEWT:380394NEWT:1692259NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:180066NEWT:67767NEWT:46835NEWT:135588NEWT:1843183NEWT:95486NEWT:58002NEWT:9103NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:146479NEWT:10306NCBITaxon:2759NEWT:1911079NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:3635NEWT:5811NEWT:235443NEWT:1480154NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:884019NEWT:169963NEWT:36329NEWT:1147787NCBITaxon:3044782NEWT:72407NEWT:9606NEWT:367830NEWT:157295NEWT:641501NEWT:178616NEWT:410289NEWT:373153NEWT:915099NEWT:74940NEWT:9721NEWT:1450511NEWT:360094NEWT:470NEWT:1313NEWT:84023NEWT:9838NCBITaxon:9615NEWT:58334NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:33952NEWT:2094720NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:178876NEWT:9940NEWT:327160NEWT:573NEWT:9031NEWT:1274420NEWT:7091NEWT:5784580000-0002-0214-285X