Windowed DIA

Summary

Name	Pub date	Scan per cycle		Window size (m/z)		MS2 window features
		MS1	MS2	Acquired	Demul.	Consecutive	Overlap (m/z)
DIA [1]	2004 Sep.	0	100	10	/	T	none
PAcIFIC [2]	2009 July	0	10	2.5	/	T	margin (1)
XDIA [4]	2010 Jan.	1	60	20	/	T	margin (1)
FT-ARM [5]	2012 Jan.	0	5	100	/	T	none
SWATH [6]	2012 Jan.	1	32	25	/	T	margin (1)
MSX [7]	2013 June	0/2	20	20	4	random	none
WiSIM-DIA [8]	2014	3	51	12	/	T	none
pSMART [10]	2014 Sep.	5	110	5,10,20	/	T	margin (1)
HRM [11]	2015 Feb.	1	19	24-222	/	T	margin (2)
SONAR [12]	2017 Sep.	200*	200*	24	2.5	T	scanning Q1
μDIA [14]	2018 July	1	120	9	3	T	one-third (3)
Staggered DIA [15]	2018 Dec.	2	20	20	10	T	one-half (10)
RTwinDIA [17]	2019 May	1	40	5	/	T	none
DIA-FAIMS [18]	2020 Feb.	1	49	13.7	/	T	margin (1)
PulseDIA [19]	2020 Sep.	1	24	5-29/11-71	/	reg. inter.	margin (1)
PASS-DIA [20]	2020 Oct.	5	75	2	/	T	none
HRMS1-DIA [21]	2020 Oct.	3	54	15	/	T	none
BoxCarmax [22]	2021 Feb.	1	30	10	2.5	reg. inter.	margin (1)
Scanning SWATH [23]	2021 Mar.	0	250*	10	2	T	scanning Q1
BoxCar DIA [24]	2021 July	4	24	20-583	/	reg. inter.	margin (1)
Zeno SWATH [25]	2022 Nov.	1	85	6-10	/	T	margin (1)
Narrow-window DIA [26]	2023	1	300	2	/	T	none

Note

• Pub date

  • the date the method was publicly released by publisher

  • WiSIM-DIA is released as a Thermo Application Note

  • Narrow-window DIA is currently a pre-print

• Scan per cycle

  • Number of finally recorded scans for MS1 or MS2 in one cycle

  • SONAR and Scanning SWATH are annotated by the numbers of bins at Q1 level

• Window size (m/z)

  • Acquired is the real window size defined in acquisition settings for instrument, and the overlapped size is eliminate (e.g. if 21 m/z widnow size is used to ensure a 1 m/z overlap within adjacent windows, its effective size is 20 m/z)

  • Demul. is the computationally demultiplexed window size (so-called demultiplexing region in [15])

• MS2 window features

  • Consecutive indicates if the MS2 windows in a cycle are defined in a continous manner (reg. inter. means regular interval)

  • Fixed indicates if all MS2 windows have the same size

  • Overlap indicates how the adjacent MS2 windows overlapped (though the adjacent windows might be not consecutive)

• All window sizes included in this document have margin overlap subtracted

Individuals

DIA

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Reference:

[1]

Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. 10.1038/nmeth705

Full name	Data-Independent Acquisition
Authors	John D Venable et al.
Lab & Company	Yates Lab
Publication date	2004, Sep.
MS instrument	LTQ
MS1 spectra per cycle	0
MS2 spectra per cycle	100
MS2 window size	10 m/z
Demultiplexing region	/
Covered mass range	400-1400 m/z
Injection times	1
Cycle time	~35 s
MS2 window features	Consecutive & fixed window size & non-overlapping windows

• Vanilla DIA scheme, with no MS1 scans, and a fixed 10 m/z window runs on pre-defined m/z range in a cycle without overlap.

PAcIFIC

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Reference:

[2]

Precursor Acquisition Independent From Ion Count: How to Dive Deeper into the Proteomics Ocean. 10.1021/ac900888s

[3]

Faster, Quantitative, and Accurate Precursor Acquisition Independent From Ion Count. 10.1021/ac103079q

Full name	Precursor Acquisition Independent From Ion Count
Authors	Alexandre Panchaud et al.
Lab & Company	Goodlett Lab
Publication date	2009 July
MS instrument	LTQ Orbitrap XL
MS1 spectra per cycle	0
MS2 spectra per cycle	100
MS2 window size	10 m/z
Demultiplexing region	/
Covered mass range	400-1400 m/z
Injection times	1
Cycle time	~35 s
MS2 window features	Consecutive & fixed window size & margin-overlapping windows (1 m/z)

• 2.5 m/z window, and a 1 m/z overlap between adjacent windows.

• The first MS2 scan in the first injection starts from a center mass of 401 m/z, and the last MS2 scan in last injection has a center mass of 1403.5 m/z.

• Requires ~67 injections and ~5 days to finish the acquisition for one sample in 2009 on a LTQ Orbitrap XL instrument, and the effiency is improved to ~2 days with a faster LTQ Orbitrap Velos in 2011.

XDIA

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Reference:

[4]

XDIA: improving on the label-free data-independent analysis. 10.1093/bioinformatics/btq031

Full name	extended DIA
Authors	Paulo C. Carvalho et al.
Lab & Company	Yates Lab
Publication date	2010, Jan.
MS instrument	LTQ-Orbitrap XL (+ETD)
MS1 spectra per cycle	1
MS2 spectra per cycle	60
MS2 window size	20 m/z
Demultiplexing region	/
Covered mass range	400-1000 m/z
Injection times	1
Cycle time	/
MS2 window features	Consecutive & fixed window size & margin-overlapping windows (1 m/z) & two scans for each window (one for ETD, one for ETD+CID)

• Each acquisition window is scaned twice, by using ETD in the first scan and followed by ETD+CAD in the second scan for ion dissociation.

FT-ARM

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Reference:

[5]

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification. 10.1021/pr2008175

Full name	Fourier Transform-All Reaction Monitoring
Authors	Chad R. Weisbrod et al.
Lab & Company	Bruce Lab
Publication date	2012, Jan.
MS instrument	LTQ-FT and LTQ Orbitrap
MS1 spectra per cycle	0
MS2 spectra per cycle	5
MS2 window size	100 m/z
Demultiplexing region	/
Covered mass range	500-1000 m/z
Injection times	1
Cycle time	~5.45 s
MS2 window features	Consecutive & fixed window size & non-overlapping windows

SWATH

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Reference:

[6]

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. 10.1074/mcp.O111.016717

Full name	Sequential Window Acquisition of all THeoretical (mass spectra)
Authors	Ludovic C. Gillet et al.
Lab & Company	Aebersold Lab
Publication date	2012, Jan.
MS instrument	TripleTOF 5600
MS1 spectra per cycle	1
MS2 spectra per cycle	32
MS2 window size	25 m/z
Demultiplexing region	/
Covered mass range	400-1200 m/z
Injection times	1
Cycle time	~3.3 s
MS2 window features	Consecutive & fixed window size & margin-overlapping windows (1 m/z)

MSX

Reference:

[7]

Multiplexed MS/MS for improved data-independent acquisition. 10.1038/nmeth.2528

Full name	MSX
Authors	Jarrett D Egertson et al.
Lab & Company	MacCoss Lab
Publication date	2013, June
MS instrument	Q Exactive
MS1 spectra per cycle	0 (or 2 for MS1 quantification)
MS2 spectra per cycle	20 (5 discrete sub-windows in each scan)
MS2 window size	20 m/z (5 * 4 m/z sub-window for ion accumulation)
Demultiplexing region	4 m/z
Covered mass range	500-900 m/z
Injection times	1
Cycle time	~3.5 s
MS2 window features	5 sub-windows in each scan are randomly picked & fixed window size & non-overlapping windows

• Actual center position of Q1 in the first 4 m/z segment is 502.4783 m/z with a window width of 4.002 m/z, agreeing with m/z distribution of precursor residue combinations.

WiSIM-DIA

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Reference:

[8]

Large-scale targeted protein quantification using wide selected-ion monitoring data-independent acquisition. Thermo Scientific Application Note 600

[9]

Application of wide selected-ion monitoring data-independent acquisition to identify tomato fruit proteins regulated by the CUTIN DEFICIENT2 transcription factor. 10.1002/pmic.201500450

Full name	Wide Selected-Ion Monitoring DIA
Authors	Reiko Kiyonami et al.
Lab & Company	Thermo Fisher Scientific GmbH
Publication date	2014
MS instrument	Orbitrap Fusion Tribrid
MS1 spectra per cycle	3
MS2 spectra per cycle	51
MS2 window size	12 m/z
Demultiplexing region	/
Covered mass range	400-1004 m/z
Injection times	1
Cycle time	~3.6 s
MS2 window features	Consecutive & fixed window size & non-overlapping windows

• MS2 scans are performed in ion trap in parallel with MS1 scan in Orbitrap

pSMART

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Reference:

[10]

Hybrid data acquisition and processing strategies with increased throughput and selectivity: pSMART analysis for global qualitative and quantitative analysis. 10.1021/pr5003017

Full name	pSMART
Authors	Amol Prakash et al.
Lab & Company	Thermo Fisher Scientific GmbH
Publication date	2014, Sep.
MS instrument	Q Exactive
MS1 spectra per cycle	5
MS2 spectra per cycle	110
MS2 window size	5 m/z window for 400-800 m/z, 10 m/z window for 800-1000 m/z, 20 m/z window for 1000-1200 m/z
Demultiplexing region	/
Covered mass range	400-1200 m/z
Injection times	1
Cycle time	~26 s
MS2 window features	Consecutive & variable window sizes & margin-overlapping windows (1 m/z)

• In each cycle, 5 HR/AM MS1 spectra are acquired every ~5 s.

HRM

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Reference:

[11]

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues. 10.1074/mcp.M114.044305

Full name	Hyper Reaction Monitoring
Authors	Roland Bruderer et al.
Lab & Company	Biognosys AG
Publication date	2015, Feb.
MS instrument	Q Exactive
MS1 spectra per cycle	1
MS2 spectra per cycle	19
MS2 window size	Variable (24-222 m/z)
Demultiplexing region	/
Covered mass range	400-1220 m/z
Injection times	1
Cycle time	~3.5 s
MS2 window features	Consecutive & variable window sizes & margin-overlapping windows (2 m/z)

SONAR

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Reference:

[12]

Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization. 10.1021/acs.jproteome.7b00464

[13]

Scanning Quadrupole Data-Independent Acquisition, Part B: Application to the Analysis of the Calcineurin-Interacting Proteins during Treatment of Aspergillus fumigatus with Azole and Echinocandin Antifungal Drugs. 10.1021/acs.jproteome.7b00499

Full name	SONAR
Authors	Arthur Moseley et al.
Lab & Company	Waters Corporation
Publication date	2017, Sep.
MS instrument	Xevo G2-XS
MS1 spectra per cycle	200
MS2 spectra per cycle	200
MS2 window size	24 m/z
Demultiplexing region	2.5 m/z
Covered mass range	400-900 m/z
Injection times	1
Cycle time	~1 s
MS2 window features	Consecutive & fixed window size & intra-overlapping windows (21.5 m/z at Q1 bin level)

μDIA

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Reference:

[14]

Micro-Data-Independent Acquisition for High-Throughput Proteomics and Sensitive Peptide Mass Spectrum Identification. 10.1021/acs.analchem.8b01026

Full name	microDIA
Authors	Michael R. Heaven et al.
Lab & Company	Norris Lab
Publication date	2018, July
MS instrument	impact II
MS1 spectra per cycle	1
MS2 spectra per cycle	120
MS2 window size	9 m/z
Demultiplexing region	3 m/z
Covered mass range	400-1115 m/z
Injection times	1
Cycle time	~3.4 s
MS2 window features	Consecutive & fixed window size & intra-overlapping windows (3 m/z)

Staggered DIA

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Reference:

[15] (1,2)

Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry. 10.1038/s41467-018-07454-w

[16]

Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows. 10.1007/s13361-018-2122-8

Full name	microDIA
Authors	Brian C. Searle et al.
Lab & Company	MacCoss Lab
Publication date	2018, Dec.
MS instrument	Q Exactive
MS1 spectra per cycle	2
MS2 spectra per cycle	20
MS2 window size	20 m/z
Demultiplexing region	10 m/z
Covered mass range	490-900 m/z
Injection times	1
Cycle time	~2.5 s
MS2 window features	Consecutive & fixed window size & inter-overlapping windows (10 m/z)

• In two-step cycles, odd-numbered cycle covers 500-900 m/z and even-numbered cycle covers 490-890 m/z.

RTwinDIA

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Reference:

[17]

Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition. 10.1007/s13361-019-02243-1

Full name	RT windowed DIA
Authors	Wenxue Li et al.
Lab & Company	Liu Lab
Publication date	2019, May
MS instrument	Orbitrap Fusion Lumos
MS1 spectra per cycle	1
MS2 spectra per cycle	40
MS2 window size	5 m/z
Demultiplexing region	/
Covered mass range	400-1000 m/z
Injection times	1
Cycle time	~3.2 s
MS2 window features	Consecutive & fixed window size & non-overlapping windows

• MS1 covers 350-1650 m/z. MS2 in 3 blocks: 400-600 m/z for RT range 0-50%; 600-800 m/z for RT range 50-75%; 800-1000 m/z for RT range 75-100%.

DIA-FAIMS

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Reference:

[18]

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients. 10.1074/mcp.TIR119.001906

Full name	DIA-FAIMS
Authors	Dorte B. Bekker-Jensen et al.
Lab & Company	Olsen Lab
Publication date	2020, Feb.
MS instrument	Orbitrap Exploris 480
MS1 spectra per cycle	1
MS2 spectra per cycle	49
MS2 window size	13.7 m/z (15k2s method)
Demultiplexing region	/
Covered mass range	361-1032.3 m/z (15k2s method)
Injection times	1
Cycle time	~2.3 s (15k2s method)
MS2 window features	Consecutive & fixed window size & margin-overlapping windows (1 m/z)

PulseDIA

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Reference:

[19]

PulseDIA: Data-Independent Acquisition Mass Spectrometry Using Multi-Injection Pulsed Gas-Phase Fractionation. 10.1021/acs.jproteome.0c00381

Full name	PulseDIA
Authors	Xue Cai et al.
Lab & Company	Guo Lab
Publication date	2020, Sep.
MS instrument	Q Exactive HF
MS1 spectra per cycle	1
MS2 spectra per cycle	24
MS2 window size	Variable 5-29 m/z for 4 injections, and variable 11-71 m/z for 2 injections
Demultiplexing region	/
Covered mass range	400-1200 m/z
Injection times	2-5
Cycle time	~2 s
MS2 window features	Discrete & variable window size & margin-overlapping windows (1 m/z)

• Each cycle has 1 MS1 scan and 24 MS2 scans. MS1 covers 390-1210 m/z, and MS2 from all injections covers 400-1200 m/z.

• The MS2 covered 800 m/z are split into 24 segments, in which 20 segments with 20 m/z width cover 400-800 m/z, and the other 4 segments cover 800-860, 860-940, 940-1060, 1060-1200 m/z.

• Each segment is equally divided into n parts, where n is the injection number, and 1 m/z overlap is added when determining the window size.

• Four window schemes are defined: 2-injection has window sizes of 11, 31, 41, 61, and 71 m/z; 3-injection has window sizes of 8, 21, 28, 41, and 48 m/z; 4-injection has window sizes of 6, 16, 21, 31, and 36 m/z; 5-injection has window sizes of 5, 13, 17, 25, and 29 m/z.

PASS-DIA

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Reference:

[20]

PASS-DIA: a data-independent acquisition approach for discovery studies. 10.1021/acs.analchem.0c02513

Full name	Precursor ion And Small Slice-DIA
Authors	Dong-Gi Mun et al.
Lab & Company	Pandey Lab
Publication date	2020, Oct.
MS instrument	Q Exactive HF
MS1 spectra per cycle	5
MS2 spectra per cycle	75
MS2 window size	2 m/z
Demultiplexing region	/
Covered mass range	350-1400 m/z
Injection times	7
Cycle time	/
MS2 window features	Consecutive & fixed window size & non-overlapping windows

• Each injection covers 150 m/z. Each cycle has 75 MS2 scans with a fixed 2 m/z window size, and MS1 scan is acquired per 15 MS2 scans.

HRMS1-DIA

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Reference:

[21]

Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies. 10.1038/s41467-020-18904-9

Full name	High-Resolution MS1-based quantitative DIA
Authors	Yue Xuan et al.
Lab & Company	Thermo Fisher Scientific GmbH
Publication date	2020, Oct.
MS instrument	Q Exactive HF
MS1 spectra per cycle	3
MS2 spectra per cycle	54
MS2 window size	15 m/z
Demultiplexing region	/
Covered mass range	400-1210 m/z
Injection times	1
Cycle time	~5.23 s
MS2 window features	Consecutive & fixed window size & non-overlapping windows

• Each cycle comprises 3 MS1 full scans and 54 sequential MS2 scans. MS1 full scans are inserted before the 1st, 18th, 35th MS2 scans. Each MS1 full scan covers whole mass range of 400-1210 m/z.

BoxCarmax

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Reference:

[22]

BoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex Samples. 10.1021/acs.analchem.0c04293

Full name	BoxCarmax
Authors	Barbora Salovska et al.
Lab & Company	Liu Lab
Publication date	2021, Feb.
MS instrument	Orbitrap Fusion Lumos
MS1 spectra per cycle	1
MS2 spectra per cycle	30
MS2 window size	10 m/z (4 * 2.5 m/z sub-windows)
Demultiplexing region	/
Covered mass range	357-1197 m/z
Injection times	4
Cycle time	~2.8 s
MS2 window features	Discrete & fixed window size & margin-overlapping windows (1 m/z)

Scanning SWATH

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Reference:

[23]

Ultra-fast proteomics with Scanning SWATH. 10.1038/s41587-021-00860-4

Full name	Scanning SWATH
Authors	Christoph B. Messner et al.
Lab & Company	Ralser Lab
Publication date	2021, Mar.
MS instrument	TripleTOF 6600
MS1 spectra per cycle	0
MS2 spectra per cycle	250
MS2 window size	10 m/z
Demultiplexing region	2 m/z
Covered mass range	400-900 m/z
Injection times	1
Cycle time	~0.52s (5 min gradient), ~0.31s (1 min gradient), ~0.28s (0.5 min gradient)
MS2 window features	Consecutive & fixed window size & intra-overlapping windows (8 m/z at Q1 bin level)

BoxCar DIA

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Reference:

[24]

MaxDIA enables library-based and library-free data-independent acquisition proteomics. 10.1038/s41587-021-00968-7

Full name	BoxCar DIA
Authors	Pavel Sinitcyn et al.
Lab & Company	Cox Lab
Publication date	2021, July
MS instrument	Orbitrap Fusion Lumos
MS1 spectra per cycle	4
MS2 spectra per cycle	24
MS2 window size	Variable (20-583 m/z)
Demultiplexing region	/
Covered mass range	350-1650 m/z
Injection times	1
Cycle time	~3.3 s
MS2 window features	Consecutive & variable window size & margin-overlapping windows (1 m/z)

• “BoxCar DIA” instrument settings were extracted from “20201006_LU1_DaIt_Aurora5_HEK1_BOXCAR_SWATH_2ul.raw” from PXD022589 accompanying with MaxDIA paper.

• Each cycle has 1 MS1 full scan, 3 tSIM scans, and 24 MS2 scans sequentially arranged. MS1 full scan covers 350-1650 m/z. 3 tSIM scans are interspersed with each other like those in BoxCar DDA, start from 350-385, 384-412, and 411-434 m/z, respectively, and end at 898-966, 965-1068, 1067-1650 m/z, respectively.

Zeno SWATH

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Reference:

[25]

High-throughput proteomics of nanogram-scale samples with Zeno SWATH MS. 10.7554/eLife.83947

Full name	Zeno SWATH
Authors	Ziyue Wang et al.
Lab & Company	Ralser Lab
Publication date	2022 Nov.
MS instrument	ZenoTOF 7600
MS1 spectra per cycle	1
MS2 spectra per cycle	85
MS2 window size	6-10 m/z
Demultiplexing region	/
Covered mass range	400-903 m/z
Injection times	1
Cycle time	/
MS2 window features	Consecutive & variable window size & margin-overlapping windows (1 m/z)

Narrow-window DIA

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Reference:

[26]

Narrow-window DIA: Ultra-fast quantitative analysis of comprehensive proteomes with high sequencing depth. 10.1101/2023.06.02.543374

Full name	Narrow-window DIA
Authors	Ulises H. Guzman et al.
Lab & Company	Olsen Lab
Publication date	2023
MS instrument	Orbitrap Astral
MS1 spectra per cycle	1
MS2 spectra per cycle	300
MS2 window size	2 m/z
Demultiplexing region	/
Covered mass range	380-980 m/z
Injection times	1
Cycle time	/
MS2 window features	Consecutive & fixed window size & non-overlapping windows