Summary of Study ST003477
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 PR002136. The data can be accessed directly via it's Project DOI: 10.21228/M8HN84 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 | ST003477 |
| Study Title | Biocrates Test |
| Study Summary | We assessed technical replicates of NIST Standard Reference Material (SRM 1950) human plasma specimens on different Biocrates MxP Quant 500 kit well-plates. In total, 9 different technical replicates on 9 different Biocrates MxP Quant 500 kit well-plates were measured. The resulting data is used as a showcase to demonstrate the utility of our MetaboSERV platform for selecting, exchanging, and visualizing metabolomics data with controlled data access. |
| Institute | Hannover Medical School |
| Department | Peter L. Reichertz Institute for Medical Informatics |
| Last Name | Zacharias |
| First Name | Helena |
| Address | Carl-Neuberg-Str. 1, 30625 Hannover, Germany |
| zacharias.helena@mh-hannover.de | |
| Phone | +49 511/532-30881 |
| Submit Date | 2024-08-09 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-10-03 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002136 |
| Project DOI: | doi: 10.21228/M8HN84 |
| Project Title: | MetaboSERV - a platform for selecting, exchanging, and visualizing metabolomics data with controlled data access |
| Project Type: | Research Publication, Software development |
| Project Summary: | The growing number of metabolomics studies, based on high-dimensional data measured by hyphenated mass spectrometry (MS) and/or nuclear magnetic resonance (NMR) spectroscopy, has sparked the creation of several public metabolomics data repositories. Each repository emphasizes different aspects regarding data selection and representation, but most offer only limited options for privacy-preserving data sharing. We present MetaboSERV, an open-source, browser-based metabolomics platform dedicated to the selection, integration and sharing of quantitative metabolomics data and metadata with controlled data access. MetaboSERV aims to aid researchers in analyzing their results by facilitating means to browse, visualize and compare data across available data sets. It provides different access control functionalities, creating an environment in which data can be shared safely in a privacy-preserving manner to support collaborative and interdisciplinary research. Furthermore, it is designed to be extensible and adaptable to existing data management infrastructures through the creation of self-managed MetaboSERV instances, for which we provide the source code and a set of pre-built Docker images. |
| Institute: | Hannover Medical School |
| Department: | Peter L. Reichertz Institute for Medical Informatics |
| Last Name: | Zacharias |
| First Name: | Helena |
| Address: | Carl-Neuberg-Str. 1, 30625 Hannover, Germany |
| Email: | zacharias.helena@mh-hannover.de |
| Phone: | +49 511/532-30881 |
| Funding Source: | Bundesministerium für Bildung und Forschung (BMBF), e:Med initiative |
| Contributors: | Tim Tucholski, Angela Maennel, Yacoub Abelard Njipouombe Nsangou, Sven Schuchardt, Matthias Gruber, Fabian Kellermeier, Katja Dettmer, Peter J. Oefner, Wolfram Gronwald, Michael Altenbuchinger, Jürgen Dönitz and Helena U. Zacharias |
Subject:
| Subject ID: | SU003605 |
| 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 | Biocrates Plate | Sample source |
|---|---|---|---|
| SA383719 | plate_1 | 1 | NIST Standard Reference Material (SRM 1950) |
| SA383720 | plate_2 | 2 | NIST Standard Reference Material (SRM 1950) |
| SA383721 | plate_3 | 3 | NIST Standard Reference Material (SRM 1950) |
| SA383722 | plate_4 | 4 | NIST Standard Reference Material (SRM 1950) |
| SA383723 | plate_5 | 5 | NIST Standard Reference Material (SRM 1950) |
| SA383724 | plate_6 | 6 | NIST Standard Reference Material (SRM 1950) |
| SA383725 | plate_7 | 7 | NIST Standard Reference Material (SRM 1950) |
| SA383726 | plate_8 | 8 | NIST Standard Reference Material (SRM 1950) |
| SA383727 | plate_9 | 9 | NIST Standard Reference Material (SRM 1950) |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO003598 |
| Collection Summary: | NIST Standard Reference Material (SRM 1950) |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR003614 |
| Treatment Summary: | no specific treatment |
Sample Preparation:
| Sampleprep ID: | SP003612 |
| Sampleprep Summary: | Samples were analyzed using the MxP® Quant 500 kit according to the kit protocol. A sample volume of 10 µL was used. It was directly added to a 96-well kit plate followed by a derivatization solution. The analytes were eluted from the plate with an extraction solvent. The extracts were split for LC and FIA analysis and diluted accordingly using either water for LC-MS/MS or a FIA solvent for FIA-MS/MS. |
Combined analysis:
| Analysis ID | AN005712 |
|---|---|
| Analysis type | MS |
| Chromatography type | Other |
| Chromatography system | ExionLC 30AD (Sciex) |
| Column | MxP Quant 500 column system (Biocrates) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | ABI Sciex 6500+ QTrap |
| Ion Mode | UNSPECIFIED |
| Units | µM |
Chromatography:
| Chromatography ID: | CH004333 |
| Chromatography Summary: | UHPLC; Column dimensions were not available from the kit manufacturer. |
| Instrument Name: | ExionLC 30AD (Sciex) |
| Column Name: | MxP Quant 500 column system (Biocrates) |
| Column Temperature: | 50°C |
| Flow Gradient: | Flow Gradient LC1: 0% B (0.25 min) --> 12% B (1.25 min) --> 17.5% B (1.2 min) --> 50% B (1.3 min) --> 100% B (0.5 min) --> stay at 100% B (0.5 min) --> 0% B (0.1 min) --> stay at 0% B (0.7 min), total 5.8 min Flow Gradient LC2: 0% B (0.25 min) --> 25% B (0.25 min) --> 50% B (1.5 min) --> 75% B (1.0 min) --> 100% B (0.5 min) --> stay at 100% B (1.5 min) --> 0% B (0.1 min) --> stay at 0% B (0.7 min), total 5.8 min |
| Flow Rate: | 0.8 mL/min, increased to 1.0 mL/min from minute 4.7 to 5.1 |
| Solvent A: | 100% water; 0.2% formic acid |
| Solvent B: | 100% acetonitrile; 0.2% formic acid |
| Chromatography Type: | Other |
MS:
| MS ID: | MS005435 |
| Analysis ID: | AN005712 |
| Instrument Name: | ABI Sciex 6500+ QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Samples were analyzed with four methods employing HPLC separation (LC) or flow injection analysis (FIA). LC1 used ionization in positive mode and scheduled MRM detection (125 transitions). LC2 used ionization in negative mode and scheduled MRM detection (69 transitions). Both FIA methods used ionization in positive mode and MRM detection (165 and 382 transitions). Data were analyzed employing the Biocrates MetIDQ software. |
| Ion Mode: | UNSPECIFIED |
