235-244

DOI: 10.6623/chem.2016022

-SWATH
*

sequential window acquisition of all theoretical

fragment ion spectra (SWATH) 2012 Ruedi Aebersold
SWATH (data independent acquisition, DIA)
(data dependent acquisition, DDA)
(multiple reaction monitoring, MRM)
SWATH (proteomics)
(peptidomics) (lipidomics) (metabolomics)

SWATH (omics)

SWATH

MRM
4
(liquid chromatography-tan-
demmass spectrometry, LC-MS/MS)

(data independent acquisition,
(shotgun strategy) DIA)

5,6-13
(data dependent acquisition, DDA) m/z ()

1
MS/MS
2,3
sequential window acqui-
sition of all theoretical fragment ion spectra (SWATH)
25 Da
DDA

(targeted strategy) (multiple reaction 2012 Ruedi Aebersold
monitoring, MRM) SWATH 5 DDA

235
-SWATH

DIA

/

Duty cycle (%) 1
Shotgun CID Q-TOF nozzle-skimmer +++/ 2 - --(7%)
nozzle-skimmer

1 1 800 Da SWATH
MSE ( Waters) QqTOF +++/ 2 +(LC: 3-4 logs) --(7%)
1
1 800 Da SWATH
All ion fragmentation Orbi-Trap +++/ 2 +(LC: 4 logs) --(7%)
(AIF)
1 1 800 Da SWATH
SWATH-MS QqTOF (25 Da) ++/3.2 ++(Intra-scan: 4 ++(89%)
100 32 25 Da (1 Da logs)
) SWATH
Data independent Ion Trap (10 20 Da) +/ 4 +(> 2log?) -(16%)
acquisition 200 20 10 Da
( Da ) SWATH
Data independent Ion Trap- (20 Da) + - --(6%)
acquisition-ETD-CAD ETD-CAD 20 Da (1 Da )
SWATH
Precursor acquisition Ion Trap (2.5 Da) - -/ 5.4 +++(LC: 7 logs) +(68%)
independent from ion LC 20 Da
count (PAcIFIC) 250 30 2.5 Da (1.5 Da
) SWATH
1
transitions

MRM (isolation window) (

DIA SWATH LC-MS/MS 26 m/z 1 m/z )
(400-1,200 m/z)
() SWATH accumulation time 100
DDAMRMSWATH 400-1,200 m/z 32
SWATH cycle time 3.2
30
SWATH

9,12
SWATH sequential window acquisition of all DIA SWATH
theoretical fragment ion spectra 2012 Ruedi 1
Aebersold m/z
25 m/z SWATH -
25 m/z (quadrupole/time-of-flight mass spectrometer, QqTOF MS)

236
-SWATH

DDAMRMSWATH DDA MS1

(collision induced dissociation, CID) MS2
MRM MS1 CID SWATH
25 Da MS1 25 Da CID
MS2 Da

mum, FWHM) 30,000

4


SWATH
15 V
5 DIA
SWATH

SWATH 25 m/z
dwell time
(400-1, 200 m/z) CID


(fragment ion interference) 5
SCIEX
TripleTOF MS/MS

MS/MS 100
MS/MS Triple TOF
2016 Heaven MR 12
15,000 (full width at half maxi- SWATH 6

237
-SWATH

6 m/z
SWATH
(signal-to-noise
ratio)

14 SWATH Zhang Y
Q1 SWATH
(variable windows)
()
SWATH

Triple TOF (AB
10%scheduled
Sciex)
SWATH
m/z (trypsin) 15
(Escherichia coli) SWATH
450 730 m/z 4465
26 m/z QqTOF MS
SWATH 400 1200 m/z SWATH
3309 QqTOFMS 16 SWATH
450 730 m/z DDA DDA

SWATH (A) (B) m/z

(cofragment peptide) b3

238
-SWATH

SWATH MS
17-20
DDA
MRM
()SWATH SWATH

MRM 4
5 SWATH SWATH (Proteomics)
MRM MRM

SWATH (quan-
SWATH titative proteomics)
SWATH 39 2013 Aebersold R
21
SWATH MS MRM (affinity purification, AP) SWATH 14-3-3
DDA insulin-PI3K-AKT 25
22SWATH N-linked
DDA SWATH (limit of quantification, LOQ) 0.0456 fmol
23,24
SWATH MRM LOQ

DDA DIA DDA MS/MS DIA

MS/MS

239
-SWATH

26
CV% 14.90% SWATH 35
N-acylethanola-
mine acid amidase protein tyrosine kinase 7 SWATH
27
SWATH HIV-1
HIV-1 SWATH
28
Hou G 2015 SUMOylationubiquitinationacetylationglycation
SWATH SUMOylation ubiquitination
MRM DNA
SWATH MRM 2014 Griffiths JR SWATH
29
Aranga M SWATH HIV-1 SUMOylation ubiquitination (isopeptide)
(monocyte-derived 38Zawadzka
macrophages, MDM) AM SWATH
(nanoparticle atazanavir, nanoATV) MRM SWATH
HIV MRM 39 2015
30Vaswani K SWATH Sidoli S SWATH (histone)
(cervicovaginal fluid, CVF) SWATH
CV < 9% 4
22
SWATH
( H3K18ac H3K23ac)
31
(Mycobacterium H3K9me2S10ph (
tuberculosis) < 0.02%)
(CV < 15%) 40Korwar AM
32
SWATH (glycated
(low biomass) (biofilm) albumin) 13
(Shewanella oneidensis) MR-1 albumin K549
(carbon cloth electrodes) K438K409K88K375 lysine
SWATH 704
33 41
(tricarboxylic cycle, TCA)
2016 Li C SWATH
LC-MS/MS 42
SWATH
959 SWATH (Peptidomics)

(apolipoproteins) SWATH
34
SWATH
35

36 37
HIV

240
-SWATH

2015 Ruedi Aebersold SWATH 2014 Roemmelt AT SWATH

(human leukocyte antigen, HLA) 382 DDA
(immunopeptidome) SWATH DDA
472015 Scheidweiler KB
HLA 43 HLA LC-QTOF SWATH 15
() 81% SWATH 47
() 25 Da 10 Da 48
13% () SWATH
3 4 44

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 CHEMISTRY (The Chinese Chemical Society, Taipei) Vol. 74, No. 3, pp. 235-244

Special Report

Novel Mass Spectrometry-Based Technique for

Quantitative Omics-SWATH

Han-Ju Chien, Yu-Ting Xue and Chien-Chen Lai*

Institute of Molecular Biology, National Chung Hsing University

ABSTRACT
With the rapid development of the mass spectrometry (MS), the technology of quantitative
analysis hasmade great progress. In 2012, Ruedi Aebersold groupdeveloped a novel MS data
acquisition mode-sequential window acquisition of all theoretical fragment ion spectra (SWATH).
SWATH aims to complement traditional mass spectrometry-based qualification and quantitation
techniques such as data dependent acquisition (DDA) and multiple reaction monitoring (MRM)
methods. SWATH utilizes data independent acquisition (DIA) strategies to increase the repro-
ducibility andcomprehensiveness of data collection andcan perform a larger number of MRM-like
experiments concurrently. SWATH can be applied to various field ofthe Omics, such as pro-
teomics, peptidomics, lipidomics, metabolomics, post-translational modification and etc.

Key words: Mass spectrometry; Quantitation; Omics; SWATH; Data independent acquisition.

244