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public_databases.Rmd
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public_databases.Rmd
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---
title: "Database provided for `metid`"
author:
- name: Xiaotao Shen PhD (https://www.shen-lab.org/)
date: "Created on 2020-03-28 and updated on `r Sys.Date()`"
output:
html_document:
df_print: paged
toc: no
pdf_document:
toc: no
vignette: >
%\VignetteIndexEntry{public_data}
%\VignettePackage{metid}
% \VignetteEngine{knitr::rmarkdown}
% \usepackage[utf8]{inputenc}
%\VignetteEncoding{UTF-8}
---
```{r, include=FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
out.width = "100%"
)
```
***
# **In-house MS2 databases from [Michael Snyder lab](http://med.stanford.edu/snyderlab.html)**
## 1. Michael Snyder HILIC databases
* <i class="fa fa-info"></i> Professor Michael Snyder's lab. More than 1,000 metabolites.
* <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/mpsnyder_hilic_ms2.rda)
## 2. Michael Snyder RPLC databases
* <i class="fa fa-info"></i> Professor Michael Snyder's lab. More than 1,000 metabolites.
* <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/mpsnyder_rplc_ms2.rda)
# **In-house MS2 databases from [Caroline Johnson lab](https://medicine.yale.edu/lab/cjohnson/)**
## 1. Caroline Johnson HILIC databases
* <i class="fa fa-info"></i> From Professor Caroline Johnson's lab.
* <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/HILIC.database)
## 2. Caroline Johnson RPLC databases
* <i class="fa fa-info"></i> From Professor Caroline Johnson's lab.
* <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/RPLC.database)
***
# **Public MS2 databases**
## 1. [HMDB database](https://hmdb.ca/downloads)
* <i class="fa fa-info"></i> HMDB database.
* <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/hmdb_ms2.rda)
## 2. [MassBank database](https://massbank.eu/MassBank/)
* <i class="fa fa-info"></i> MassBank database.
* <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/massbank_ms2.rda)
## 3. [MoNA database](https://mona.fiehnlab.ucdavis.edu/)
* <i class="fa fa-info"></i> MoNA database.
* <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/mona_ms2.rda)
## 4. [Orbitrap database](https://mona.fiehnlab.ucdavis.edu/)
* <i class="fa fa-info"></i> Orbitrap database from MoNA.
* <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/orbitrap_database0.0.3.rda)
## 5. [Fiehn HILIC database](https://fiehnlab.ucdavis.edu/staff/kind/publications)
* <i class="fa fa-info"></i> HILIC MS2 database from Fiehn lab.
* <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/fiehn_hilic_database0.0.3.rda)
<!-- ### 6. Exposome database -->
<!-- * <i class="fa fa-info"></i> Some chemical exposome database -->
<!-- * <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/exposureDatabase) -->
> If you need this database, please contact shenxt@stanford.edu.
***
# **Public MS1 databases**
## 1. [HMDB MS1 database](https://hmdb.ca/downloads)
* <i class="fa fa-info"></i> HMDB MS1 database.
* <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/hmdb_ms1.rda)
## 2. [KEGG MS1 database](https://www.genome.jp/kegg/compound/)
* <i class="fa fa-info"></i> KEGG MS1 database.
* <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/kegg_ms1.rda)
<!-- ### 4. [Foodb database](https://foodb.ca/downloads) -->
<!-- * <i class="fa fa-info"></i> Foodb MS1 database. -->
<!-- * <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/hmdbMS1Database0.0.1) -->
## 3. [T3DB database](http://www.t3db.ca/downloads)
* <i class="fa fa-info"></i> T3DB MS1 database.
* <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/t3db_ms1.rda)
## 4. [Blood exposome database](https://bloodexposome.org/#/download)
* <i class="fa fa-info"></i> Blood exposome MS1 database.
* <i class="fa fa-download"></i> [Download here](https://www.shen-lab.org/ms2_data/bloodexposome_ms1.rda)
# **Session information**
```{r,eval=TRUE,warning=FALSE, R.options="", message=FALSE, cache=TRUE}
sessionInfo()
```