Metabolite Identification
Raw data were imported into Progenesis QI v3.0 (Waters Corporation, Milford, MA, USA) for preprocessing, including baseline filtering, peak detection, integration, retention time correction, and peak alignment. A data matrix containing retention time, *m/z*, and peak intensity was obtained. Subsequently, feature identification was performed within the same software by matching the MS and MS/MS spectral information against metabolite databases. The mass error tolerance was set to <10 ppm, and metabolites were further confirmed based on MS/MS match scores. The main databases used were public repositories such as the Human Metabolome Database (HMDB, http://www.hmdb.ca/) and METLIN (https://metlin.scripps.edu/), as well as an in house custom database.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["Chromatographic Conditions
Column: ACQUITY UPLC HSS T3 (100 mm × 2.1 mm i.d., 1.8 µm; Waters, Milford, MA, USA).
Mobile phase A: 95% water + 5% acetonitrile (containing 0.1% formic acid).
Mobile phase B: 47.5% acetonitrile + 47.5% isopropanol + 5% water (containing 0.1% formic acid).
Flow rate: 0.40 mL/min.
Injection volume: 10 µL.
Column temperature: 40 °C.
"],"publication":["Gut Microbiota-Mediated Tryptophan Metabolism Plays Dual Effects in Diffuse Large B-Cell Lymphoma via Regulating 3-IAA/5-HTP Balance and Antitumor Immunity."],"submitter_affiliation":["qilu hospital"],"submitter_name":["Na He"],"organism_part":["blood plasma"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Metabolite Extraction Protocol
1. Precisely transfer 100 uL of each sample into a 1.5 mL microcentrifuge tube.
2. Add 300 uL of extraction solvent (methanol : acetonitrile = 1:1, v/v) containing four internal standards (including L2chlorophenylalanine at 0.02 mg/mL).
3. Vortex mix for 30 s, then perform ultrasonic extraction at 5 C and 40 kHz for 30 min.
4. Incubate the samples at -20 C for 30 min.
5. Centrifuge at 13,000 x g for 15 min at 4 C. Transfer the supernatant and evaporate to dryness under a gentle nitrogen stream.
6. Reconstitute the residue with 100 uL of reconstitution solution (acetonitrile : water = 1:1, v/v).
7. Vortex mix for 30 s, followed by ultrasonic extraction at 5 C and 40 kHz for 5 min.
8. Centrifuge at 13,000 x g for 10 min at 4 C. Transfer the supernatant into an autosampler vial with a glass insert for LC MS analysis.
9. For quality control (QC) samples, aliquot 20 uL of the supernatant from each individual sample and pool them into a single mixed QC sample, which will be injected periodically throughout the analytical run.
"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15570"],"author":["Na He. qilu hospital. hena7081@163.com."],"data_transformation_protocol":["Data Preprocessing
Raw metabolomics data, comprising both experimental samples and quality control (QC) samples, were subjected to a series of preprocessing steps. First, metabolic features with >20% missing values within any group were removed. For the remaining missing values, the minimum value across all samples was imputed. Next, total sum normalization was applied to each sample to correct for variations in total metabolite abundance among samples. Subsequently, features with a relative standard deviation (RSD) >30% in QC samples were filtered out to ensure analytical reproducibility. Finally, the preprocessed data were log10 transformed to reduce skewness and meet the distributional assumptions required for subsequent multivariate statistical analyses.
Detailed procedures are as follows:
Missing value filtering: Features with >20% missing values in each group were excluded to maintain data quality.
Missing value imputation: Remaining missing values were replaced with the minimum value observed across all samples, which is suitable for features below the detection limit.
Data normalization: Total sum normalization was performed per sample to eliminate the influence of total metabolite abundance differences and enhance comparability between samples.
QC validation: To assess analytical stability and data reproducibility, features with RSD >30% in QC samples were discarded; only those with good reproducibility were retained.
Data transformation: The normalized data were log10 transformed to reduce skewness and approximate a normal distribution, thereby improving the reliability of subsequent multivariate statistical analyses.
"],"study_factor":["DLBCL","Control"],"submitter_email":["hena7081@163.com"],"sample_collection_protocol":["Sample Collection & Storage Procedure
Peripheral blood plasma samples were collected from newly diagnosed lymphoma patients and healthy normal controls. No therapeutic interventions had been administered to any subject prior to blood collection. Blood was drawn into EDTA containing tubes and centrifuged (e.g., 1500×g for 15 min at 4 °C) to separate plasma, which was then aliquoted and immediately frozen in liquid nitrogen. All samples were stored at –80 °C until metabolite extraction. On the day of extraction, plasma aliquots were thawed on ice.
"],"omics_type":["Metabolomics"],"study_design":["ultra-performance liquid chromatography-mass spectrometry","Metabolomics","blood plasma","untargeted analysis","AB SCIEX TripleTOF 5600+","untargeted metabolites","Homo sapiens","diffuse large B-cell lymphoma","AB SCIEX","experimental sample"],"curator_keywords":["ultra-performance liquid chromatography-mass spectrometry","Metabolomics","blood plasma","untargeted analysis","AB SCIEX TripleTOF 5600+","untargeted metabolites","Homo sapiens","diffuse large B-cell lymphoma","AB SCIEX","experimental sample"],"mass_spectrometry_protocol":["Mass Spectrometry Conditions
Ion source: Electrospray ionization (ESI), operated in both positive ion and negative ion modes.
Mass range: *m/z* 50–1000.
Gas settings:
Nebulizer gas (GS1) and auxiliary heating gas (GS2): 50 psi each.
Curtain gas (CUR): 30 psi.
Ion source temperature: 550 °C.
Ion spray voltage: +5000 V (positive mode) and –4000 V (negative mode).
Interface heater: ON.
Declustering potential (DP): 80 V.
Collision energy: 40 ± 20 eV (i.e., collision energy spread with a center of 40 eV).
Cycle time: 510 ms.
"],"additional_accession":[]},"is_claimable":false,"name":"Gut Microbiota-Mediated Tryptophan Metabolism Plays Dual Effects in Diffuse Large B-Cell Lymphoma via Regulating 3-IAA/5-HTP Balance and Antitumor Immunity","description":"Timing-dependent tryptophan diets differentially modulate DLBCL outcomes via microbiota-derived 3-IAA (pre-inoculation, anti-tumor) versus 5-HTP (post-inoculation, pro-tumor), with pectin restoring microbial balance to enable a timed tryptophan-pectin precision nutrition strategy for enhanced immunotherapy.","dates":{"publication":"2026-09-07","submission":"2026-09-06"},"accession":"MTBLS15570","cross_references":{}}