Summary of Study ST001104
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 PR000716. The data can be accessed directly via it's Project DOI: 10.21228/M8496H 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 | ST001104 |
| Study Title | Seryl-leucine core 1 O-glycosylated peptide (SLC1G) identification |
| Study Summary | An untargeted metabolomics approach was utilized to determine urinary metabolites that could serve as small molecule biomarkers for treatment response to standard tuberculosis treatment. However, the majority of metabolites that most accurately distinguished patient samples at time of diagnosis from those at one month after the start of therapy lacked structural identification. The detection of unknown metabolite structures is a well-known limitation of untargeted metabolomics, and underscores a need for continued elucidation of novel metabolite structures. In this study, we sought to define the structure of a urine metabolite with an experimentally determined mass of 202.1326 Da, classified as molecular feature (MF) 874.3547. Using mass spectrometry combined with enzymatic digestions, the metabolite was structurally characterized as a seryl-leucine core 1 O-glycosylated peptide (SLC1G) of human origin. |
| Institute | Colorado State University |
| Last Name | Fitzgerald |
| First Name | Bryna |
| Address | 3185 Rampart Rd |
| blfitz@colostate.edu | |
| Phone | 9704918905 |
| Submit Date | 2018-09-26 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2019-01-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000716 |
| Project DOI: | doi: 10.21228/M8496H |
| Project Title: | Evaluation of TB Treatment Response Biomarkers |
| Project Type: | Directed MS analysis |
| Project Summary: | Directed MS analysis of promising treatment response biomarkers in TB patient urine. |
| Institute: | Colorado State University |
| Department: | Department of Microbiology, Immunology, and Pathology |
| Laboratory: | Belisle |
| Last Name: | Fitzgerald |
| First Name: | Bryna |
| Address: | 3185 Rampart Rd, Fort Collins, CO, 80521, USA |
| Email: | blfitz@colostate.edu |
| Phone: | 9704918905 |
| Funding Source: | NIH U01 AI-115619 |
Subject:
| Subject ID: | SU001149 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample Type |
|---|---|---|
| SA075182 | SLC1G_only.d | Enriched SLC1G |
| SA075184 | SLC1G+a2-368.d | Enriched SLC1G after treatment with a2-3,6,8 neuraminidase |
| SA075185 | SLC1G+both.d | Enriched SLC1G after treatment with a2-3,6,8 neuraminidase and O-glycosidase |
| SA075186 | SLC1G+both-r002.d | Enriched SLC1G after treatment with a2-3,6,8 neuraminidase and O-glycosidase for comparison with seryl-leucine standard |
| SA075187 | SLC1G+both_10.d | Enriched SLC1G after treatment with a2-3,6,8 neuraminidase and O-glycosidase for comparison with seryl-leucine standard |
| SA075183 | SLC1G+a2-3.d | Enriched SLC1G after treatment with a2-3 neuraminidase |
| SA075188 | 7728_CE20.d | Patient urine |
| SA075189 | SL_10.d | Seryl-leucine Standard |
| SA075190 | SL-r002.d | Seryl-leucine Standard |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO001143 |
| Collection Summary: | Urine was collected and frozen at -20 for storage. Prior to analysis, urine was thawed and centrifuged to remove particulates. |
| Sample Type: | Urine |
Treatment:
| Treatment ID: | TR001163 |
| Treatment Summary: | Urine, SLC1G enriched from urine, and seryl-leucine synthetic standard were analyzed by LC-MS and LC-MS/MS |
Sample Preparation:
| Sampleprep ID: | SP001156 |
| Sampleprep Summary: | Urine was thawed on ice and centrifuged to remove particulates prior to analysis. |
Combined analysis:
| Analysis ID | AN001796 | AN001797 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 1200 | Agilent 1200 |
| Column | Atlantis T3 reverse-phase C18 (150 x 2.1mm,3.5um) | Atlantis T3 reverse-phase C18 (150 x 2.1mm,3.5um) |
| MS Type | ESI | ESI |
| MS instrument type | TOF | QTOF |
| MS instrument name | Agilent 6230 TOF | Agilent 6520 QTOF |
| Ion Mode | POSITIVE | POSITIVE |
| Units | counts | m/z |
Chromatography:
| Chromatography ID: | CH001268 |
| Instrument Name: | Agilent 1200 |
| Column Name: | Atlantis T3 reverse-phase C18 (150 x 2.1mm,3.5um) |
| Column Temperature: | 30 |
| Flow Gradient: | 100% Solvent A to 90% Solvent B |
| Flow Rate: | 0.25 ml/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001657 |
| Analysis ID: | AN001796 |
| Instrument Name: | Agilent 6230 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 2000 V |
| Dry Gas Flow: | 11 L/min |
| Fragment Voltage: | 120 V |
| Nebulizer: | 40 psi |
| Octpole Voltage: | 750 V |
| Skimmer Voltage: | 60 V |
| Analysis Protocol File: | SLC1G_Identification_Methods.docx |
| MS ID: | MS001658 |
| Analysis ID: | AN001797 |
| Instrument Name: | Agilent 6520 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 2000 V |
| Collision Energy: | 10 V |
| Dry Gas Flow: | 8 L/min |
| Fragment Voltage: | 120 V |
| Nebulizer: | 45 psi |
| Octpole Voltage: | 750 V |
| Scanning Cycle: | 1.2 spectra/sec |
| Scanning Range: | 100-1700 m/z |
| Skimmer Voltage: | 60 V |
| Analysis Protocol File: | SLC1G_Identification_Methods.docx |
