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Kratochwill"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":["Not available"],"submitter_keywords":["Tmt","Peritoneal dialysis"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD050859"],"tissue":["Peritoneum"],"sample_protocol":["Digestion was performed using single-pot, solid-phase enhanced sample preparation (SP3). Briefly, 100 µg of each sample and the internal standard the reduced (10 mM DTT for 1h at 56°C) and alkylated (55 mM IAA, 30 min at RT) proteins were bound to SP3 beads (10:1 beads:protein ratio, GE Healthcare), washed with 80% ethanol and acetonitrile, and subjected to on-bead digestion with trypsin/LysC (1:25 protease:protein ratio, Promega) overnight at 37°C in 50 mM ammonium bicarbonate, pH 8.5 (Sigma). After elution peptides were desalted using C18 macrospin columns (30−300μg, The Nest Group), dried in a vacuum concentrator and reconstituted in 100 mM TEAB, pH 8.5 (Fluka). Peptide concentration was determined using the Colorimetric Peptide Assay (Thermo Fisher Scientific) according to the protocol. Labeling with TMTpro (Thermo Fisher Scientific) was performed according to the instructions provided by the manufacturer. TMTpro reagents were reconstituted with acetonitrile and each sample was labeled with one vial of TMTpro reagent. After incubation for 1h at RT the reaction was quenched by addition of 5% hydroxylamine (Sigma) in TEAB and incubation for 15 min at RT. Labeling efficiency was determined by making a pool out of a small aliquot of each sample and analysis via LC-MS and ProteomeDiscoverer. Pooled samples were concentrated and desalted with C18 macrospin columns (30−300μg, The Nest Group). Eluates were dried in a vacuum concentrator and reconstituted in 20 mM ammonia formate buffer, pH 10 before fractionation at basic pH. Two dimensional liquid chromatography was performed by reverse-phase chromatography at high and low pH. In the first dimension peptides were separated on a Gemini-NX C18 (150 x 2mm, 3 µm, 110 A, Phenomenex, Torrance, USA) in 20 mM ammonia formate buffer, pH 10 and eluted over a 32 min gradient from 0% to 30% solvent B followed by 6 min at 100% solvent B at 50 µl/min using an Ultimate 3000 RSLC micro system (Thermo Fisher Scientific) equipped with a fraction collector. Thirty-six fractions were collected in a time-based manner (every 30s). Organic solvent was removed in a vacuum concentrator and samples were reconstituted in 0.1% trifluoroacetic acid. Fractions were analyzed at low pH on an Ultimate 3000 RSLC nano coupled directly to a Q Exactive mass spectrometer (both Thermo Fisher Scientific). Samples were injected into a reversed-phase C18 column (50 cm x 75 µm i.d., packed in-house) and eluted with a gradient of 6% to 65% mobile phase B over 94 min by applying a flow rate of 230 nl/min. MS scans were performed in the range from m/z 375–1650 at a resolution of 70,000 (at m/z = 200). MS/MS scans were performed choosing a top 10 method for peptide identification and relative quantification of TMT reporter ions with following parameters: resolution 35,000; normalized collision energy 33%; isolation width 1.2 m/z; dynamic exclusion 90s."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["The acquired raw MS data files were processed and analyzed using ProteomeDiscoverer (v2.4.0.305, Thermo Fisher). SequestHT was used as search engine and following parameters were chosen: database: Homo sapiens (SwissProt, downloaded on 2020-08-31, without isoforms); enzyme: trypsin; max. missed cleavage sites: 2; static modifications: TMTpro (K and peptide N-terminus) and carbamidomethyl (C); dynamic modifications: oxidation (M), deamidation (N, Q), acetyl (protein N-terminus), Met-loss (M) and Met-loss+Acetyl (M); precursor mass tolerance: 10 ppm; fragment mass tolerance: 0.025 Da. For reporter ion quantification the most intense m/z in a 20 ppm window around the theoretical m/z was used. Correction of isotopic impurities for reporter ion intensities was applied. Only unique peptides were used for quantification, which was based on S/N values with an average S/N threshold of 10. Normalization was based on total peptide amount and scaling mode on all average. Only peptides and proteins with FDR <0.01 are reported and single peptide IDs were excluded from the dataset."],"omics_type":["Proteomics"],"labhead":["Dr Klaus Kratochwill"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Medical University of Vienna"],"species":["Homo Sapiens (human)"],"publication":["42006205 Herzog R, Daniel-Fischer L, Eibensteiner F, Sobieszek IJ, Unterwurzacher M, Sacnun JM, Uhl PKT, Lang E, Wagner A, König F, Alper SL, Davies LC, Aufricht C, Vychytil A, Kratochwill K. Local Immunometabolic Intervention With Alanyl-Glutamine Resolves Peritoneal Dialysis-Induced Immune Cell Dysfunction. Kidney Int Rep. 2026 11(5):106342 10.1016/j.ekir.2026.106342"],"submitter_mail":["klaus.kratochwill@meduniwien.ac.at"],"submitter_affiliation":["Medical University of Vienna"],"submitter_country":["Austria"],"pubmed_abstract":["

Introduction

Peritoneal dialysis (PD) is the most prevalent home-based dialysis therapy. However, chronic exposure to metabolically imbalanced high-glucose PD fluids is associated with infectious complications and morphological changes that limit PD duration and patient survival. Here, we analyzed interactions among peritoneal cell immune function, inflammation, and glucose metabolism in a prospective cohort study of patients on PD.

Methods

In 117 patients (mean follow-up: 2.15 years), samples from peritoneal equilibration tests (PETs) were assessed for interleukin (IL)-6 levels as a measure of peritoneal inflammation, and ex vivo toll-like receptor (TLR)-stimulated cytokine release as a measure of immune cell function. In addition, proteomic profiling and targeted metabolomics (1000 metabolites) were performed on peritoneal effluents. Coincubation experiments using patient effluents from a single-center randomized controlled trial (RCT) (n = 20 patients) and immune cells from healthy donors were also conducted to assess effluent-induced immune modulation. Samples from a multicenter RCT (n = 37 patients) were used as a validation cohort.

Results

Peritoneal inflammation correlated negatively with peritoneal cell immune function and positively with increased risk of subsequent peritonitis (hazard ratio: 3.8). Patients with higher peritoneal inflammation had an altered peritoneal metabolomic profile, with significant perturbation of glucose and amino acid metabolism. Immunometabolic intervention with alanyl-glutamine (AlaGln) supplementation of PD fluid restored immune cell function specifically in patients with high peritoneal inflammation, highlighting the potential to prevent subsequent infections.

Conclusion

These results provide the first direct, longitudinal evidence linking immunometabolism with peritoneal glucose exposure, local inflammation, as well as impaired peritoneal cell function and infection in a human PD cohort. Metabolic intervention designed to restore adequate peritoneal cell immune function represents a novel therapeutic approach with promise for improved clinical outcomes in chronic PD."],"pubmed_title":["Local Immunometabolic Intervention With Alanyl-Glutamine Resolves Peritoneal Dialysis-Induced Immune Cell Dysfunction."],"pubmed_authors":["Herzog Rebecca R, Daniel-Fischer Lisa L, Eibensteiner Fabian F, Sobieszek Isabel J IJ, Unterwurzacher Markus M, Sacnun Juan Manuel JM, Uhl Phoebe K T PKT, Lang Elisabeth E, Wagner Anja A, König Franz F, Alper Seth L SL, Davies Luke C LC, Aufricht Christoph C, Vychytil Andreas A, Kratochwill Klaus K"],"additional_accession":[]},"is_claimable":false,"name":"TMTpro-SP3-LC-MS analysis of peritoneal dialysis effluent of a phase 2 randomized clinical trial","description":"Peritoneal dialysis (PD) is a modality of renal replacement therapy in which the high volumes of available PD effluent (PDE) represents a rich source of biomarkers for monitoring disease and therapy. Although this information could help guiding the management of PD patients, little is known about the potential of PDE to define pathomechanism-associated molecular signatures in PD. Here we use a high-performance multiplex proteomics approach based on depletion of highly abundant plasma proteins and enrichment of low abundance proteins for PDE samples from PD patients of a phase 2 randomized clinical trial, who received either standard PD fluid or a novel PD fluid (added alanyl-glutamine (AlaGln)) in an open-label, randomized, single-center, cross-over clinical trial.","dates":{"publication":"2026-04-27","submission":"2024-03-21"},"accession":"PXD050859","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:1131","NEWT:35795","NEWT:2042546","NEWT:259447","NEWT:295546","NEWT:1334565","NEWT:625351","NEWT:258594","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:247480","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:2315688","NEWT:1073882","NEWT:6819","NEWT:475174","NEWT:1599","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:12215","NEWT:1590","NEWT:10034","NEWT:33114","NEWT:1596","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:3767","NEWT:1589","NEWT:135622","NEWT:4615","NEWT:672127","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:1582","NEWT:3760","NEWT:1584","NEWT:36630","NEWT:1585","NEWT:383379","NEWT:381198","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:1392488","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:7719","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:49928","NEWT:3349","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:410658","NEWT:5516","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:345076","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:1310173","NEWT:200795","NEWT:2579791","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:260499","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:2649329","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:150808","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:3714","NCBITaxon:37162","NEWT:3715","NEWT:2065263","NEWT:177437","NEWT:717966","NEWT:10891","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:3704","NEWT:244366","NEWT:1246791","NEWT:176597","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:9006","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:926571","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:485","NEWT:56636","NEWT:2499525","NEWT:2853422","NEWT:487","NEWT:1538553","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:45972","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:1502","NEWT:128017","NEWT:2836","NEWT:376686","NEWT:237610","NEWT:95486","EFO:0001352","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:11757","NEWT:987059","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:1509","NEWT:491","NEWT:460523","NEWT:45954","NEWT:235443","NEWT:1579","NEWT:1757312","NEWT:85694","NEWT:109786","NEWT:108458","NEWT:5936","NEWT:321967","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:415978","NEWT:1255228","NEWT:410289","NEWT:191701","NEWT:373153","NEWT:1640278","NEWT:472","NEWT:940825","NEWT:29459","NEWT:529507","NEWT:1071661","NEWT:28128","NEWT:470","NEWT:41122","NEWT:5911","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:11723","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:29488","NEWT:215402","NEWT:1547","NEWT:1290454","NEWT:3726","NEWT:906914","NEWT:81231006","NEWT:28141","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:3728","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:548","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:2126348","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:542","NEWT:2903","NEWT:185579","NEWT:872227","NEWT:13076","NEWT:2587410","NEWT:207340","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:2126337","NEWT:550","NEWT:33941","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:42410","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:771870","NEWT:51338","NEWT:9995","NEWT:575412","NEWT:28112","NEWT:49012","NEWT:6493","NEWT:10832","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:64657","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:5147","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:5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