笔记本 ｜ My notes
Preface
Disclaimer
Writing style
Acknowledgments
I Analytical Instrument
1
Bruker SolariX XR
1.1
Introduction
1.2
Practical user manual
1.2.1
Sensitivity test for MALDI
1.2.2
Sensitivity test for ESI
1.2.3
Check the isolation and fragmentation
1.2.4
Check mass resolution (elemental composition)
1.2.5
Bakeout: for vacuum maintenance
1.2.6
Some parameters
1.3
Trouble shooting
2
MALDI2-Orbitrap
2.1
Introduction
2.1.1
The Instrument
2.2
Pratical User manual
2.2.1
MALDI2 Imaging Workflow
2.3
Touble shooting
2.3.1
Cannot turn on Explore one laser
2.3.2
Ion intensity is too low
2.3.3
Not all samples are analysed in batch mode
2.3.4
CryLas laser is not working
2.3.5
Crylas laser does not generate any extra ions in MALDI2
2.3.6
Scan duration time inconsistency
2.4
Calibration
2.4.1
The MS calibration failed for Ion Mass/Res.
3
DESI MRM
3.1
Introduction
3.2
Pratical user manual
3.2.1
Ion Transfer Capillary Installation
3.2.2
Setting contact closure for DESI imaging
3.3
Trouble shooting
3.3.1
DESI stage is not moving (properly)
3.3.2
Vacuum lost
3.3.3
DESI source optimization
4
Waters SYNAPT G2-S
4.1
Warm-up knowledge
4.1.1
What is an Inlet Method?
4.1.2
What is an MS method?
4.1.3
What is tune method?
4.1.4
What is a Sample List?
4.2
Running a LC-MS project
4.3
Pratical user manual
4.3.1
Calibration
5
Q-Exactive Orbitrap Focus LC-MS/MS
5.1
Introduction
5.2
Practical user manual
5.2.1
Start N2 generator
5.2.2
Purge pump
5.2.3
Wash needle
5.2.4
Turn on UV lamp
5.2.5
Select column and set column temperature
5.2.6
Set autosampler temperature
5.2.7
Equilibrate column
5.2.8
Check solvent levels
5.2.9
Build Sequence
5.3
Trouble shooting
5.3.1
Direct control software indicates that seal wash bottle is dry, even through there is enough seal wash solution
5.3.2
Pump Code 4099 Pressure fallen below lower limit.
5.3.3
LCMS system contamination by dibutylamine
II Chemoinformatics
6
Data Conversion
6.1
Introduction
6.1.1
Thermo RAW files
6.1.2
Extracting only MS/MS data
6.2
Waters MSE Raw Data
6.3
How to verify your conversion
6.4
Other file conversion method
7
Basic Shell Commonds
7.1
Introduction
7.2
Usage
7.2.1
Manipulating files and directories
7.2.2
Manipulating data
8
Shiny
8.1
Introduction
8.2
Cheatsheet
8.2.1
ui: Layout
8.2.2
ui: Input
8.2.3
ui: output
8.2.4
Example
9
Tidyverse
9.1
Introduction
9.2
tidyr
9.3
dplyr
9.4
purrr
9.4.1
Eliminating for loops using map() function
9.4.2
Working with lists using purrr package
9.4.3
Other useful functions
9.5
stringer
10
data.table
10.1
Introduction
References
Published with bookdown
Metabolomics and Chemoinformatics
Chapter 10
data.table
10.1
Introduction
data.table
is the number one choice for handling large datasets in R.
library
(data.table)