Summary of Study ST002462
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001589. The data can be accessed directly via it's Project DOI: 10.21228/M89H8W This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
Study ID | ST002462 |
Study Title | Tryptophan metabolites in human sera on a defined diet |
Study Summary | Trp metabolites circulating in serum could provide insight into homeostatic activity of AHR, and we wished to know if the observations in mice could be replicated in humans. Previous work by our group identified AHR activators in human feces, yet it is not clear if these activators are also present in circulation. To address this question, we quantified Trp metabolites in human serum. To mitigate the variable effect of diet on metabolite profiles, we analyzed sera samples collected from study participants fed a defined diet. As with the previously discussed mouse sera, targeted metabolomics was performed on serum samples using LC-MS. |
Institute | Pennsylvania State University |
Last Name | DONG |
First Name | FANGCONG |
Address | 309 Life Sciences Building, University Park, PA 16802 |
fxd93@psu.edu | |
Phone | 8146990203 |
Submit Date | 2023-01-27 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzML |
Analysis Type Detail | LC-MS |
Release Date | 2023-02-06 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR001589 |
Project DOI: | doi: 10.21228/M89H8W |
Project Title: | Tryptophan metabolites in human serum |
Project Type: | MS quantitative study |
Project Summary: | Trp metabolites circulating in serum could provide insight into homeostatic activity of AHR, and we wished to know if the observations in mice could be replicated in humans. Previous work by our group identified AHR activators in human feces, yet it is not clear if these activators are also present in circulation. To address this question, we quantified Trp metabolites in human serum. To mitigate the variable effect of diet on metabolite profiles, we analyzed sera samples collected from study participants fed a defined diet. As with the previously discussed mouse sera, targeted metabolomics was performed on serum samples using LC-MS. |
Institute: | The Pennsylvania State University |
Last Name: | DONG |
First Name: | FANGCONG |
Address: | 309 Life Sciences Building, State college, PA, 16802, USA |
Email: | fxd93@psu.edu |
Phone: | 8146990203 |
Subject:
Subject ID: | SU002552 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Species Group: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
mb_sample_id | local_sample_id | diluted factor |
---|---|---|
SA246379 | std5 | 1 |
SA246380 | std3 | 1 |
SA246381 | std1 | 1 |
SA246382 | std6 | 1 |
SA246383 | std2 | 1 |
SA246384 | std4 | 1 |
SA246385 | std7 | 1 |
SA246386 | std10 | 1 |
SA246387 | std9 | 1 |
SA246388 | std8 | 1 |
SA246389 | 16DP1 | 2.5 |
SA246390 | 30DP1 | 2.5 |
SA246391 | 62DP1 | 2.5 |
SA246392 | 40DP3 | 2.5 |
SA246393 | 51DP1 | 2.5 |
SA246394 | 63DP3 | 2.5 |
SA246395 | 63DP2 | 2.5 |
SA246396 | 30DP2 | 2.5 |
SA246397 | 60DP3 | 2.5 |
SA246398 | 47DP1 | 2.5 |
SA246399 | 29DP2 | 2.5 |
SA246400 | 14DP1 | 2.5 |
SA246401 | 12DP1 | 2.5 |
SA246402 | 52DP3 | 2.5 |
SA246403 | 25DP2 | 2.5 |
SA246404 | 62DP3 | 2.5 |
SA246405 | 29DP1 | 2.5 |
SA246406 | 58DP3 | 2.5 |
SA246407 | 58DP2 | 2.5 |
SA246408 | 37DP2 | 2.5 |
SA246409 | 20DP2 | 2.5 |
SA246410 | 17DP1 | 2.5 |
SA246411 | 14DP2 | 2.5 |
SA246412 | 52DP1 | 2.5 |
SA246413 | 25DP3 | 2.5 |
SA246414 | 12DP3 | 2.5 |
SA246415 | 54DP3 | 2.5 |
SA246416 | 61DP2 | 2.5 |
SA246417 | 60DP2 | 2.5 |
SA246418 | 47DP2 | 2.5 |
SA246419 | 17DP2 | 2.5 |
SA246420 | 20DP3 | 2.5 |
SA246421 | 55DP1 | 2.5 |
SA246422 | 61DP1 | 2.5 |
SA246423 | 37DP3 | 2.5 |
SA246424 | 54DP2 | 2.5 |
SA246425 | 55DP2 | 2.5 |
SA246426 | 40DP1 | 2.5 |
SA246427 | 50DP3 | 2.5 |
SA246428 | 16DP3 | 2.5 |
Showing results 1 to 50 of 50 |
Collection:
Collection ID: | CO002545 |
Collection Summary: | human sera were processed by ice-cold methanol. |
Sample Type: | Blood (serum) |
Treatment:
Treatment ID: | TR002564 |
Treatment Summary: | Thawed on ice, 25 µL of serum sample, was mixed with 100 µL extraction solvent of ice-cold methanol containing indole-3-acetic acid-d4 and kynurenic acid-d5. Mixture was vortexed and incubated at −20 °C for 30 min. Following centrifugation at 12,000 × g for 15 min at 4℃, 90 µL supernatant was collected and subsequently evaporated to dryness (Thermo Scientific, Waltham, MA) and dissolved in 45 µL of 10% acetonitrile containing 1 µM chlorpropamide. After centrifugation at 12,000 × g for 15 min at 4℃, supernatants were transferred to autosampler vials for LC-MS analysis. |
Sample Preparation:
Sampleprep ID: | SP002558 |
Sampleprep Summary: | 40 selected trial participants were fed a standardized isocaloric diet (representative of an average American macronutrient intake) to achieve weight maintenance for four weeks At the end of the diet period and following a 12 h fast (and avoidance of over-the-counter medication), serum was collected, stored at -80℃ and subjected to analysis by metabolomics. |
Combined analysis:
Analysis ID | AN004017 |
---|---|
Analysis type | MS |
Chromatography type | Reversed phase |
Chromatography system | Shimadzu 20AD |
Column | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
MS Type | ESI |
MS instrument type | Triple TOF |
MS instrument name | ABI Sciex 5600 TripleTOF |
Ion Mode | POSITIVE |
Units | uM |
Chromatography:
Chromatography ID: | CH002967 |
Instrument Name: | Shimadzu 20AD |
Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
Column Temperature: | 55 |
Flow Gradient: | The initial condition were 97% A and 3 % B, increasing to 45% B at 10 min, 75% B at 12 min where it was held at 75% B until 17.5 min before returning to the initial conditions. |
Flow Rate: | 0.25 mL/min |
Solvent A: | 100% water; 0.1% formic acid |
Solvent B: | 100% acetonitrile; 0.1% formic acid |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS003764 |
Analysis ID: | AN004017 |
Instrument Name: | ABI Sciex 5600 TripleTOF |
Instrument Type: | Triple TOF |
MS Type: | ESI |
MS Comments: | Peakview was used for data analysis |
Ion Mode: | POSITIVE |