Shiny从入门到入定——16-Escaping the graph

安装

metid包能够用于in-house代谢物库构建，并可利用MS2 spectra进行代谢物鉴定。metid自带数据库，来自于公共数据库的整合。

if(!require(remotes)){
install.packages("remotes")
}
remotes::install_github("tidymass/metid")

建库

构建内部库

质谱数据准备

将标准品原始质谱数据用ProteoWizard转换为mzXM格式.

标准品信息表

将标准品信息整理至csv格式表格中，参考如下。
共11列：“Lab.ID”, “Compound.name”, “mz”, “RT”, “CAS.ID”, “HMDB.ID”, “KEGG.ID”, “Formula”, “mz.pos”, “mz.neg”, “Submitter”。也可以添加更多的信息，如“Family”, “Sub.pathway” 和“Note”。

Lab.ID: 不可重复

mz: 化合物准确的mass

RT: 保留时间，以秒为单位

mz.pos: 正离子模式下化合物的mz，如M+H。可设为NA

mz.neg: 负离子模式下化合物的mz，如M-H。可设为NA

Submitter: 个人或组织名称，可设为NA

新建目录database_construction，将正离子数据放在database_construction/POS中，将负离子数据放在database_construction/NEG中，标准品信息表metabolite.info_RPLC.csv放在database_construction中。

注意：每个文件名必须包含碰撞能（collision energy），如test_NCE25.mzXML。

建库

library(metid)
datapath<-file.path("./database_construction")
mydb <- construct_database(
    path = datapath,
	version = "0.0.1",
	metabolite.info.name = "metabolite.info_RPLC.csv",
	source = "my lab",
	link = "http://xxx.com",
	creater = "someone",
	email = "x@126.com",
	rt = TRUE, # Do the metabolites have RT information or not?
	mz.tol = 15, # m/z tolerance for the match between metabolites and precursor m/z of MS2 spectra.
	rt.tol = 30, # RT tolerance for the match between metabolites and precursor m/z of MS2 spectra.
	threads = 10
)

# 保存数据库
save(mydb, file="mydb")

注意：保存时前后名字必须一样。

构建公共库

安装massdatabase

remotes::install_github("tidymass/massdatabase")

可将msp格式的数据库转换为metid数据库。目前有bug：Error in `dplyr::select()`: ! Can’t subset columns that don’t exist. ✖ Column `Name` doesn’t exist.

bug解决前可以下载已经构建好的公共库：Database provided for metid。

MassBank

下载最新的release MassBank_NIST.msp，将其放在当前目录下。

setwd("C:/Users/liu/Downloads")
library(metid)
massbank_database_2022.12.01 <- construct_mona_database(
  file = "MassBank_NIST.msp",
  path = ".",
  version = "2022.12.01",
  source = "MassBank",
  link = "https://github.com/MassBank/MassBank-data/releases",
  creater = "Hualin Liu",
  email = "LHL371@126.com",
  rt = FALSE,
  threads = 15
)

save(massbank_database_2022.12.01, file = "massbank_database_2022.12.01")

MoNA

下载对应数据库，如此处下载LC-MS Spectra (153,242 spectra)，截至2023.04.16。

library(metid)
mona_database_2023.04.16 <- construct_mona_database(
  file = "MoNA-export-LC-MS_Spectra.msp",
  path = ".",
  version = "2023.04.16",
  source = "MoNA",
  link = "https://mona.fiehnlab.ucdavis.edu/",
  creater = "Hualin Liu",
  email = "LHL371@126.com",
  rt = FALSE,
  threads = 10
)

save(mona_database_2023.04.16, file = "mona_database_2023.04.16")

library(massdatabase)

data <- massdatabase::read_msp_data("MoNA-export-LC-MS_Spectra.msp", source = "mona")

massdatabase::convert_mona2metid(data = data, path = ".", threads = 10)

参考

• Construct in-house MS2 datbase using metid
• Construct public MS2 datbase using metid

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