Summary of project PR001915
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 PR001915. The data can be accessed directly via it's Project DOI: 10.21228/M86137 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Project ID: | PR001915 |
| Project DOI: | doi: 10.21228/M86137 |
| Project Title: | Evaluation of a python-centric metabolomics data processing pipeline based on Asari. |
| Project Summary: | To standardize metabolomics data analysis and facilitate future computational developments, it is essential is have a set of well-defined templates for common data structures. Here we describe a collection of data structures involved in metabolomics data processing and illustrate how they are utilized in a full-featured Python-centric pipeline. We demonstrate the performance of the pipeline, and the details in annotation and quality control using large-scale LC-MS metabolomics and lipidomics data and LC-MS/MS data. Multiple previously published datasets are also reanalyzed to showcase its utility in biological data analysis. This pipeline allows users to streamline data processing, quality control, annotation, and standardization in an efficient and transparent manner. This work fills a major gap in the Python ecosystem for computational metabolomics. The uploaded datasets include previously unreleased datasets used for the evaluation of this pipeline including two large plasma datasets taken from recipients of one of two herpes zoster vaccines, analyzed as 17 separate batches, and a lipidomics dataset collected on a subset of these patients. |
| Institute: | Jackson Laboratory for Genomic Medicine |
| Laboratory: | Shuzhao Li Laboratory |
| Last Name: | Joshua |
| First Name: | Mitchell |
| Address: | 10 Discovery Dr, Farmington CT 06032 |
| Email: | joshua.mitchell@jax.org |
| Phone: | 8608372474 |
| Funding Source: | NIH grants U01 CA235493 (NCI), R01 AI149746 and AI149746 S1 (NIAID), and UM1 HG012651 (NHGRI). |
| Publications: | Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline (BioRxiv) Joshua Mitchell, Yuanye Chi, Maheshwor Thapa, Zhiqiang Pang, Jianguo Xia, Shuzhao Li; doi: https://doi.org/10.1101/2024.02.13.580048 |
| Contributors: | Joshua Mitchell, Yuanye Chi, Maheshwor Thapa, Shuzhao Li |
Summary of all studies in project PR001915
| Study ID | Study Title | Species | Institute | Analysis(* : Contains Untargted data) | Release Date | Version | Samples | Download(* : Contains raw data) |
|---|---|---|---|---|---|---|---|---|
| ST003075 | HZV029 TwoPhase Metabolomics and Lipidomics | Homo sapiens | Jackson Laboratory for Genomic Medicine | MS* | 2024-05-24 | 1 | 140 | Uploaded data (1G)* |
| ST003109 | HZV029 Metabolomics | Homo sapiens | Jackson Laboratory for Genomic Medicine | MS* | 2024-05-24 | 1 | 3408 | Uploaded data (28.1G)* |
