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Lundstrom"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Antigen","Pisa","Antibody"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD065457"],"tissue":["Monocyte"],"sample_protocol":["Preparations PISA-AAI - using three proteins. TNF-α, (0.19µM), INX (0.58µM) and human serum albumin (HSA, 0.19µM) were prepared in triplicates as follows: 1) TNF-α and HSA, 2) INX and HSA, as well as 3) TNF-α, INX and HSA. Similar samples were prepared with DG-INX and Fab-INX instead of INX. All samples were supplemented with 1% protease inhibitors, incubated for 40min (20°C, 300rpm), and then thermally treated and ultracentrifuged as described below. Mononuclear cells were isolated from leukocyte concentrate obtained from fresh adult blood. Monocytes were then treated for 24 h with or without 100 ng/ml LPS at 37°C, to obtain control and LPS-treated monocytes.  Cells were lysed by five freeze-thaw cycles followed by incubation for 30 min at 4°C in PBS with 0.1% NP40, and probe sonication. The cell lysate supernatants were collected following centrifugation at 10,000 g for 10 min at 4°C. The control monocytes lysates (CML) and LPS-treated monocytes lysates (LML) were stored at -80°C until further processing. To CML (0.8 mg/ml), samples of TNFα (0.08 µM) were added and incubated for 40 min at 20°C, either alone or with 0.31 µM INX, DG-INX or Fab-INX. For the gradient experiment, TNFα (0.08 µM) with or without INX (0.31 µM) were mixed together with either HSA or CML at different concentrations (0, 0.0125, 0.05, 0.2, 0.8mg/ml) and then incubated for 40 min (20°C, 300 rpm). LML samples (0.8 mg/mL) were incubated for 40 min at 20°C either alone or with 0.31µM INX, DG-INX or Fab-INX. In intact cell experiments, following LPS treatment PBS, INX or Fab-INX were added to final concentration of 0.1 mg/ml and incubated for 1 h.   PISA: Samples were distributed into 16 aliquots that were heated at 16 temperature points from 50 to 78°C for 3 min and then left to rest at 25°C for 6 min and then snap frozen. The aliquots for each sample were pooled. For the intact cells, NP-40 protein detergent was added to a final concentration of 0.4%, and the sample was shaken at 300 rpm for 1 h at 4°C. Five freeze-thaw cycles were then performed to obtain the cell lysate. All samples were ultracentrifuged for 30 min at 4°C. The supernatants were collected. For the individual protein mixture experiments, 310 µL of the supernatant was taken out per sample and 20 µL of an internal standard (0.4 mg/ml myoglobin and 0.6 mg/ml trypsinogen) added. For the protein gradient experiments, aliquots of 300 µL (samples: 0, 0.125 and 0.05 mg/mL), 200 µL (samples: 0.2 mg/mL) and 100 µL (samples: 0.8 mg/mL) of the supernatant was taken out and 20 µL of an internal standard added. The samples were prepared for proteomics analysis as described below. For the experiments on cell lysate and intact cells, the protein concentration of the supernatant following ultracentrifugation was measured, and an equal amount of protein (50 µg per sample) was used for all proteomics analyses. Samples were reduced, alkylated and digested by standard protocols. Samples were then aceton precipitated at -20°C overnight. The pellet was resuspended, digested with LysC (6 h, 30°C and with trypsin (37°C, 16 h). Digests were labeled using 10-plex or 16-plex tandem mass tag according to the manufacturer’s instructions, pooled and desalted. Samples were then dried and stored at -80°C until, depending on the sample complexity, either processed directly by LC-MS/MS analysis or first fractionated by High pH Reversed Phase Fractionation (in 24-48 fractions) and then analysed. Fractions were dried and stored at -80°C until LC-MS/MS analysis. LC−MS/MS Analysis. Analyses were performed using an UltiMate 3000 nanoUPLC system connected online to an Exploris 480 or a Lumos Orbitrap mass spectrometer equipped with an EASY nanoSpray source (all - Thermo Fisher Scientific). Peptide separation was performed using an EASY-Spray C18 reversed-phase nano LC column (Acclaim PepMap RSLC; length, 50 cm; inner diameter, 2 μm; particle size, 2 μm; pore size, 100 Å; Thermo Fisher Scientific) at 55°C with a flow rate of 300 nL/min. Peptides were separated using a binary solvent system consisting of 0.1% formic acid, 2% acetonitrile (solvent A) and 0.1% FA and  98% acetonitrile  (solvent B). Peptides were eluted by the gradient 2−27% B, followed by a ~15 min washing step (27−95% B), and a ~10 min re-equilibration step (2% B). Depending on sample complexity, the total running time varied between 120, 150 and 240 min. Mass spectra were in the positive ion mode acquired in a mass to charge (m/z) range of 375−1500 with a nominal resolution of 120,000 at m/z 200. MS/MS spectra were obtained in the data dependent acquisition mode with a dynamic exclusion time of previously selected precursor ions of 45 s. Most abundant peptide ions were selected for HCD with a normalized collision energy value set at 33 or 35%. The tandem MS spectra were acquired at a nominal resolution of 45,000 or 50,000. The fixed first m/z was 100, and the isolation window was 1.6 m/z units."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["The raw LC-MS/MS data were analyzed by Proteome Discoverer (PD, version 3.1) with TMTplex as isobaric labeling mass tag. Using Sequest search engine, the MS/MS data were matached against the Uniprot human proteome reference database (20,306 entries) supplemented with 1) the INX-heavy and INX-light chains, 2) the sequences of the internal standards trypsinogen (Bo taurus) and myoglobin (Equus caballus) and 3) a common contaminant database.  Reversed sequences of the above were concatenated for controlling the false discovery rate (FDR). Peptide mass error tolerance was set at 10 ppm, while MS/MS fragment mass accuracy was set at 0.02 Da. Cysteine carbamidomethylation was used as a fixed modification; TMT-related modifications, methionine oxidation, asparagine and glutamine deamidation were used as variable modifications. Trypsin was selected as enzyme specificity with a maximum of two missed cleavages. For the samples containing three proteins and the concentration gradient, a fixed PSM validator (PD node) value of 0.05 was used as a filter. For other complex samples, Percolator (PD node) with 1% FDR was used as a filter. After removing contaminants, only proteins above the FDR threshold with at least one unique peptide and quantified with at least two peptides were included in the final data set.  Statistical Analysis. Protein abundances in individual protein samples were normalized to the internal standards and for the gradient samples (300 µL (samples: 0, 0.125 and 0.05 mg/mL), 200 µL (samples: 0.2 mg/mL) and 100 µL (samples: 0.8 mg/mL), additionally adjusted for the difference in sample volume (i.e. 1/3, 1/2, 1/1).  Protein abundances for cell lysates and intact cells were normalized to the total protein abundance in the respective sample. For all samples, the abundance of each protein or peptide was then scaled by dividing it by the average abundance in the control samples. For individual protein samples, univariate statistical analysis was performed for normalized protein abundance using two-tailed Student’s t test, with the significance threshold set at 0.05. For the proteome-level experiments, at first peptide abundances were evaluated using Student’s t test. Then p-values of the top 3 most significant peptides for each protein were then combined according to Fisher’s method. The FDR values for proteins were corrected for multiple hypotheses according to the Storey Tibshirani method. Final protein ranking was done based on the absolute value of the log2 fold-change of the protein abundance between the test groups multiplied by -log10 of the corrected p-values of significant proteins."],"omics_type":["Proteomics"],"labhead":["Roman Zubarev"],"instrument_platform":[""],"labhead_affiliation":["Division of Chemistry I, MBB, Karolinska Institutet"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["susanna.lundstrom@ki.se"],"publication":["Not available"],"submitter_affiliation":["Division of Chemistry I\nDepartment of Medical Biochemistry & Biophysics\nKarolinska Institutet"],"submitter_country":["Sweden"],"additional_accession":[]},"is_claimable":false,"name":"Proteome integral solubility alteration assay for monitoring antibody-antigen interactions in cells","description":"Proteome Integral Solubility Alteration (PISA) assay is normally used for characterization of the interactions between a small molecule and the cellular proteome. Here we modified PISA uniquely to identify the antigen (tumor necrosis factor alpha) in activated monocytes using the monoclonal antibody Infliximab.","dates":{"publication":"2026-05-20","submission":"2025-06-25"},"accession":"PXD065457","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","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: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:192875","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:633149","NEWT:10239","NEWT:44685","NEWT:161934","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:118698","NEWT:1616117","NEWT:263","NEWT:118696","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","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: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: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:353152","NEWT:8496","NEWT:27448","NEWT:40674","NEWT:1194669","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:214053","NEWT:80863","NEWT:105231","NEWT:52638","NEWT:57075","NEWT:4097","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:9785","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NCBITaxon:780","NCBITaxon:1502","NEWT:6282","NEWT:1134506","NEWT:38783","NEWT:4006","NEWT:6426","NCBITaxon:5476","NEWT:6669","NEWT:9935","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