Benchmark data sets

Summary table

Year	Ref.	No.	Short desc.	Target	Background	Instrument
2014	[1]	1	SGS	422 SIS peptides	None / yeast / HeLa	TTOF 5600
2015	[2]	1	UPS1	UPS1	None	TTOF 5600
		2	UPS2	UPS2	None	TTOF 5600
		3	UPS2 spike	UPS2	Tryptic E. coli	TTOF 5600
2016	[3]	1	HYE124	Tryptic yeast+ecoli	Tryptic HeLa	TTOF 5600+/6600
		2	HYE110	Tryptic yeast+ecoli	Tryptic HeLa	TTOF 6600
2017	[4]	1	SynHeavyPhos	579 SIS phosphopeptides	Tryptic HEK293	TTOF 5600+
2017	[5]	1	HYEC	Tryptic yeast+ecoli+celegans	Tryptic HeLa	QE HF
2018	[6]	1	SynPhos96	96 NS phosphopeptides	Tryptic HEK293	QE HF Plus
2020	[7]	1	MixPhos	Yeast phosphoproteome	HeLa phosphoproteome	QE HF-X
		2	SynPhos200+	200+ NS phosphopeptides	Yeast phosphoproteome	QE HF-X
		3	Phos-stoich	Partial-dephos yeast phosproteome	HeLa phosphoproteome	QE HF-X
2020	[8]	1	HY13 diaPASEF	Tryptic yeast	Tryptic HeLa	timsTOF Pro
2021	[9]	1	HYE124 diaPASEF	Tryptic yeast+ecoli	Tryptic HeLa	timsTOF Pro
2021	[10]	1	SynPhos166	166 NS phosphopeptides	Tryptic yeast	Fusion Lumos
2021	[11]	1	UPS1 spike	UPS1	Tryptic E. coli	Orbitrap Fusion
2022	[12]	1	HYE124	Tryptic yeast+ecoli	Tryptic K562	TTOF 5600
		2				TTOF 6600+
		3				Synapt G2-Si
		4				QE HF-X
		5				Synapt XS
		6				timsTOF Pro
2022	[13]	1	HYE plexDIA	Tryptic yeast+ecoli	Tryptic U-937 or Jurkat	QE
2022	[14]	1	HY12 Zeno	Tryptic yeast	Tryptic K562	ZenoTOF 7600
2022	[15]	1	HE 4cond	Tryptic E. coli	Tryptic human lymph nodes	Orbitrap Eclipse
2023	[16]	1	MY 7cond	Tryptic mouse brain membrane	Tryptic yeast	QE HF/timsTOF Pro
2023	[17]	1	B57	HLA-B*57:01	Tryptic HeLa	Orbitrap Fusion
2023	[18]	1	BSA mDIA	Tryptic BSA	None	Exploris 480
		2	HYE mDIA	Tryptic yeast+ecoli	Tryptic HeLa	timsTOF HT
2023	[19]	1	UPS2 spike	UPS2	Tryptic yeast	QE HF

Note

• Target

  • SIS: stable isotope-labeled standard (synthetic peptides in all cases)

  • NS: non-labeled standard (synthetic peptides in all cases)

Individuals

OpenSWATH SGS

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Reference:

[1]

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. 10.1038/nbt.2841

Authors:

Röst et al.

Year:

2014

Dataset 1:

Short name	SWATH-MS Gold Standard (SGS)
Repository ID	PASS00289
MS instrument	TTOF 5600
Acquisition method	25 m/z wide-window SWATH
Target sample	422 SIS peptides
Background sample	Water / yeast BY4741 tryptic digest / HeLa tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	Pure SIS / SIS + yeast background / SIS + human background. SIS concentration in each sample from 1x to 512x. 3 replicates.
Additional runs	DDA runs for pure SIS peptides

DIA-Umpire UPS

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Reference:

[2]

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. 10.1038/nmeth.3255

Authors:

Tsou et al.

Year:

2015

Dataset 1:

Short name	UPS1
Repository ID	PXD001587
MS instrument	TTOF 5600
Acquisition method	25 m/z wide-window SWATH (long MS1 ion accumulation (250 ms) or not (50 ms))
Target sample	UPS1
Background sample	/
PTM	/
Other sample	/
Brief design	Pure UPS1. 3 replicates.
Additional runs	/

Dataset 2:

Short name	UPS2
Repository ID	PXD001587
MS instrument	TTOF 5600
Acquisition method	25 m/z wide-window SWATH (long MS1 ion accumulation (250 ms))
Target sample	UPS2
Background sample	/
PTM	/
Other sample	/
Brief design	Pure UPS2. 3 replicates.
Additional runs	DDA runs for pure UPS2

Dataset 3:

Short name	UPS2 spike-in
Repository ID	PXD001587
MS instrument	TTOF 5600
Acquisition method	25 m/z wide-window SWATH (long MS1 ion accumulation (250 ms) or not (50 ms))
Target sample	UPS2
Background sample	coli tryptic digest
PTM	/
Other sample	/
Brief design	UPS2 + E. coli background. 3 replicates.
Additional runs	/

LFQBench

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Reference:

[3]

A multicenter study benchmarks software tools for label-free proteome quantification. 10.1038/nbt.3685

Authors:

Navarro et al.

Year:

2016

Dataset 1:

Short name	HYE124
Repository ID	PXD002952
MS instrument	TTOF 5600+ / TTOF 6600
Acquisition method	25 m/z wide-window SWATH / 64 variable wide-window SWATH
Target sample	Tryptic digests of yeast / E. coli
Background sample	HeLa tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	A: HYE 65/30/5; B: HYE 65/15/20. 3 replicates for each sample.
Additional runs	H/Y/E each has 3 DDA runs.

Dataset 2:

Short name	HYE110
Repository ID	PXD002952
MS instrument	TTOF 6600
Acquisition method	25 m/z wide-window SWATH / 12.5 m/z wide-window SWATH / 32 variable wide-window SWATH / 64 variable wide-window SWATH
Target sample	Tryptic digests of yeast / E. coli
Background sample	HeLa tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	A: HYE 67/30/3; B: HYE 67/3/30. 3 replicates for each sample.
Additional runs	/

IPF SIS phosphopeptides

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Reference:

[4]

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. 10.1038/nbt.3908

Authors:

Rosenberger et al.

Year:

2017

Dataset 1:

Short name	SynHeavyPhos
Repository ID	PXD004573
MS instrument	TTOF 5600+
Acquisition method	64 variable wide-window SWATH
Target sample	579 synthetic SIS phosphopeptides
Background sample	HEK293 tryptic digest
PTM	Phosphorylation
Other sample	Biognosys iRT peptides (C18)
Brief design	Synthetic + HEK293 background. Total 13 dilution ratios 1:0, 1:1, …, 1:127. Single injection without replicate.
Additional runs	DDA runs for pure synthetic phosphopeptides. 3 replicates.

HYEC

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Reference:

[5]

Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results. 10.1074/mcp.RA117.000314

Authors:

Bruderer et al.

Year:

2017

Dataset 1:

Short name	HYEC
Repository ID	PXD005573
MS instrument	QE HF
Acquisition method	Variable wide-window DIA
Target sample	Tryptic digests of Yeast / E. coli / C. Elegans
Background sample	HeLa tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	1) Small fold change sample set: H 1:1; Y 1:1.2; E 1.3:1; C 1:1.1. 2) Large fold change sample set: H 1:1; Y 1.6:1; E 1:4; C 1:2. Each sample has 3 replicates.
Additional runs	A DDA library in Spectronaut .kit format is available.

Specter synthetic phospho

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Reference:

[6]

Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics. 10.1038/nmeth.4643

Authors:

Peckner et al.

Year:

2018

Dataset 1:

Short name	SynPhos
Repository ID	PXD006722
MS instrument	QE HF Plus
Acquisition method	56 x 22 m/z inter-cycle overlapping-window DIA (11 m/z shift)
Target sample	96 NS phosphopeptides
Background sample	HEK293 tryptic digest
PTM	Phosphorylation
Other sample	/
Brief design	NS phosphopeptides + HEK293 background. Total 5 samples with synthetic concentrations from 1x to 16x. 3 replicates.
Additional runs	DDA runs of all five spiked-in samples with 1 injection

HY phospho / synthetic phospho / Phospho-stoichiometry

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Reference:

[7]

Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries. 10.1038/s41467-020-14609-1

Authors:

Bekker-Jensen et al.

Year:

2020

Dataset 1:

Short name	Mixed phosphoproteome
Repository ID	PXD014525
MS instrument	QE HF-X
Acquisition method	14 m/z wide-window DIA
Target sample	Ti-IMAC enriched yeast tryptic digest
Background sample	Ti-IMAC enriched HeLa tryptic digest
PTM	Phosphorylation
Other sample	Biognosys iRT peptides (C18)
Brief design	Tryptic digests of yeast BY4742 and HeLa are mixed in 5 ratios of 0.25:1, 0.5:1, 1:1, 1.5:1, and 2:1, and mixed samples are Ti-IMAC enriched. Each sample has 6 replicates.
Additional runs	In addition to 3 yeast only and 3 HeLa only DIA runs, all DIA runs have their corresponding DDA runs with same injection numbers.

Dataset 2:

Short name	SynPhos200p
Repository ID	PXD014525
MS instrument	QE HF-X
Acquisition method	14 m/z wide-window DIA
Target sample	Multi-source NS phosphopeptides
Background sample	Ti-IMAC enriched yeast tryptic digest
PTM	Phosphorylation
Other sample	Biognosys iRT peptides (C18)
Brief design	Five sources of synthetic phosphopeptides: JPT (SpikeMix PTM-kit 52 1001098; SpikeMix PTM-kit 54 1001100) and Sigma-Aldrich (MS PhosphoMix 1 Light MSP1L, MS PhosphoMix 2 Light MSP2L, MS PhosphoMix 3 Light MSP3L). All phosphopeptides are mixed and spiked into yeast phosphoproteome in 4 dilution concentrations: 1x, 10x, 100x, and 1000x. Each sample has 3 replicates.
Additional runs	All DIA runs have their corresponding DDA runs with same injection numbers.

Dataset 3:

Short name	Phospho-stoichiometry
Repository ID	PXD014525
MS instrument	QE HF-X
Acquisition method	14 m/z wide-window DIA
Target sample	Ti-IMAC enriched yeast tryptic digest with or without phosphatase treatment
Background sample	Ti-IMAC enriched HeLa tryptic digest
PTM	Phosphorylation
Other sample	Biognosys iRT peptides (C18)
Brief design	After yeast tryptic digest was Ti-IMAC enriched, half was phosphatase treated while another half was mock treated. Two treated samples are mixed and spiked into HeLa tryptic phosphoproteome background, and formed expected phosphorylation stoichiometry of 1%, 10%, 50%, 90%, and 99%. Each final sample has 5 replicates.
Additional runs	All DIA runs have their corresponding DDA runs with same injection numbers.

HY13 diaPASEF

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Reference:

[8]

diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition. 10.1038/s41592-020-00998-0

Authors:

Meier et al.

Year:

2020

Dataset 1:

Short name	HY13 diaPASEF
Repository ID	PXD017703 (ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/12/PXD017703)
MS instrument	timsTOF Pro
Acquisition method	diaPASEF 16 scans
Target sample	Yeast tryptic digest
Background sample	HeLa tryptic digest
PTM	/
Other sample	/
Brief design	A: H/Y 200/45; B: H/Y 200/15. 3 replicates
Additional runs	Fractionated yeast and HeLa samples are analyzed by ddaPASEF.

HYE124 diaPASEF

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Reference:

[9]

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

Authors:

Sinitcyn et al.

Year:

2021

Dataset 1:

Short name	HYE124 timsTOF
Repository ID	PXD022589
MS instrument	timsTOF Pro
Acquisition method	diaPASEF 16 scans
Target sample	Tryptic digests of Yeast / E. coli
Background sample	HeLa tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	A: HYE 65/30/5; B: HYE 65/15/20. Triplicate injections for each sample.
Additional runs	ddaPASEF runs for three species individually. Sample of each species are off-line fractionated to 5 fractions, and two injections are performed for each fraction. Stored in PXD022582.

DIA-GPS 166 NS phosphopeptides

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Reference:

[10]

A data-independent acquisition-based global phosphoproteomics system enables deep profiling. 10.1038/s41467-021-22759-z

Authors:

Kitata et al.

Year:

2021

Dataset 1:

Short name	SynPhos166
Repository ID	PXD019797
MS instrument	Fusion Lumos
Acquisition method	10 m/z wide-window DIA
Target sample	166 NS phosphopeptides
Background sample	Yeast tryptic digest
PTM	Phosphorylation
Other sample	Biognosys iRT peptides (C18)
Brief design	NS phosphopeptides + yeast background. Total 5 samples with synthetic phosphopeptide concentrations from 1x to 20x. 3 replicates.
Additional runs	3 DDA runs and 3 DIA runs of pure synthetic phosphopeptides.

UPS1 Orbi multiple acquisition methods

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Reference:

[11]

Extensive and Accurate Benchmarking of DIA Acquisition Methods and Software Tools Using a Complex Proteomic Standard. 10.1021/acs.jproteome.1c00490

Authors:

Gotti et al.

Year:

2021

Dataset 1:

Short name	UPS1 spike-in
Repository ID	PXD026600
MS instrument	Orbitrap Fusion
Acquisition method	8 m/z wide-window / 15 m/z wide-window / 8 m/z inter-cycle overlapping window (4 m/z shift) / 8 m/z and 15 m/z variable wide-window
Target sample	UPS1
Background sample	coli tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	UPS1 + E. coli background. Total 8 samples with UPS1 concentrations from 1x to 500x. 3 replicates.
Additional runs	48 DDA runs for 48 fractionated E. coli samples and 1 DDA run for UPS1+E. coli sample

HYE124 multiple instruments and acquisition methods

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Reference:

[12]

A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics. 10.1038/s41597-022-01216-6

Authors:

Van Puyvelde et al.

Year:

2022

Dataset 1:

Short name	HYE124-5600
Repository ID	PXD028735
MS instrument	TTOF 5600
Acquisition method	64 variable wide-window SWATH
Target sample	Tryptic digests of Yeast / E. coli
Background sample	Human K562 tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	A: HYE 65/30/5; B: HYE 65/15/20.
Additional runs	1) 3 DDA runs for each species, resulted in total 9 runs. 2) 8 narrow-window DIA injections with 2 m/z window size.

Dataset 2:

Short name	HYE124-6600
Repository ID	PXD028735
MS instrument	TTOF 6600+
Acquisition method	1) 99 variable windowed SWATH. 2) Scanning SWATH 5 m/z window (1 m/z Q1 bin).
Target sample	Tryptic digests of Yeast / E. coli
Background sample	Human K562 tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	A: HYE 65/30/5; B: HYE 65/15/20.
Additional runs	1) 3 DDA runs for each species, resulted in total 9 runs. 2) 8 narrow-window scanning SWATH injections with 1 m/z window size (0.2 m/z Q1 bin).

Dataset 3:

Short name	HYE124-G2Si
Repository ID	PXD028735
MS instrument	Synapt G2-Si
Acquisition method	UDMSE
Target sample	Tryptic digests of Yeast / E. coli
Background sample	Human K562 tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	A: HYE 65/30/5; B: HYE 65/15/20.
Additional runs	3 DDA runs for each species, resulted in total 9 runs.

Dataset 4:

Short name	HYE124-HFX
Repository ID	PXD028735
MS instrument	QE HF-X
Acquisition method	8 m/z inter-cycle overlapping-window DIA (4 m/z shift)
Target sample	Tryptic digests of Yeast / E. coli
Background sample	Human K562 tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	A: HYE 65/30/5; B: HYE 65/15/20.
Additional runs	1) 3 DDA runs for each species, resulted in total 9 runs. 2) 8 narrow-window DIA injections with 4 m/z inter-cycle overlapping windows (2 m/z shift).

Dataset 5:

Short name	HYE124-XS
Repository ID	PXD028735
MS instrument	Synapt XS
Acquisition method	SONAR
Target sample	Tryptic digests of Yeast / E. coli
Background sample	Human K562 tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	A: HYE 65/30/5; B: HYE 65/15/20.
Additional runs	1) 3 DDA runs for each species, resulted in total 9 runs. 2) 8 narrow-window SONAR injections.

Dataset 6:

Short name	HYE124-timsTOF
Repository ID	PXD028735
MS instrument	timsTOF Pro
Acquisition method	diaPASEF 16 scans
Target sample	Tryptic digests of Yeast / E. coli
Background sample	Human K562 tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	A: HYE 65/30/5; B: HYE 65/15/20.
Additional runs	3 ddaPASEF runs for each species, resulted in total 9 runs.

HYE plexDIA

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Reference:

[13]

Increasing the throughput of sensitive proteomics by plexDIA. 10.1038/s41587-022-01389-w

Authors:

Derks et al.

Year:

2022

Dataset 1:

Short name	plexDIA HYE124/063/066
Repository ID	PXD029531 (ftp://massive.ucsd.edu/v01/MSV000089093)
MS instrument	QE
Acquisition method	5 MS1-inserted 25 variable wide-window DIA / 40 variable wide-window DIA
Target sample	Tryptic digests of Yeast / E. coli
Background sample	Human tryptic digest (U-937 or Jurkat)
PTM	/
Other sample	/
Brief design	A: non-labeled E. coli 20%, yeast 15%, U-937 65%; B: mTRAQ4 E. coli 5%, yeast 30%, U-937 65%; C: mTRAQ8 E. coli 30%, yeast 5%, Jurkat 65%
Additional runs	All DIA runs have their corresponding DDA runs with same injection numbers.

HY12 Zeno SWATH

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Reference:

[14]

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

Authors:

Wang et al.

Year:

2022

Dataset 1:

Short name	HY12 Zeno SWATH
Repository ID	PXD036786 (ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/12/PXD036786)
MS instrument	ZenoTOF 7600
Acquisition method	85 variable windowed DIA (6-10 m/z window size)
Target sample	Yeast tryptic digest
Background sample	K562 tryptic digest
PTM	/
Other sample	/
Brief design	A: HY 30/35; B: HY 30/17.5. Each sample has 3 replicates.
Additional runs	/

HE 4 conditions Orbi

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Reference:

[15]

Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity. 10.1038/s41467-022-30094-0

Authors:

Fröhlich et al.

Year:

2022

Dataset 1:

Short name	HE4Cond
Repository ID	EGAD00010002223 (request required)
MS instrument	Orbitrap Eclipse
Acquisition method	8 m/z inter-cycle overlapping-window DIA (4 m/z shift)
Target sample	coli tryptic digest
Background sample	92 tryptic digests from 92 human lymph nodes
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	Human tissue samples are from 92 different individuals, and 4 groups are formed with 23 samples in each. 4 groups have different amounts of spiked E. coli digest: no E. coli as control, 1:25, 1:12, and 1:6. Each sample is injected once and total 92 DIA data were acquired.
Additional runs	1) From each group, 3 samples are picked, and all 12 samples are mixed into one. The pooled sample is fractionated and fractions are further pooled in groups of two, and 10 pooled samples are acquired by DDA. 2) The pooled samples were also acquired by narrow-window DIA with a 2 m/z isolation window and total 6 injections to cover 400-1000 m/z.

MY 7 conditions Orbi+timsTOF

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Reference:

[16]

Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics. 10.1038/s41467-022-35740-1

Authors:

Lou et al.

Year:

2023

Dataset 1:

Short name	MY7Cond
Repository ID	PXD034709
MS instrument	QE HF / timsTOF Pro
Acquisition method	Variable wide-window DIA / diaPASEF 16 scans
Target sample	Tryptic digest of mouse brain membrane proteome
Background sample	Yeast tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	Mouse brain membrane protein digests were spiked into a yeast proteome background in seven defined proportions, yielding one reference and six mixtures with fixed mouse protein ratios relative to the reference: 1:4, 1:2, 2:3, 1:1, 3:2, and 2:1. Each sample is prepared in five replicates.
Additional runs	Mouse and yeast peptide digestions are first offline pre-fractionated to 8 fractions for each. 16 DDA runs and 16 diaPASEF runs are acquired on respective instruments.

Immunopeptidomics

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Reference:

[17]

Benchmarking Bioinformatics Pipelines in Data-Independent Acquisition Mass Spectrometry for Immunopeptidomics. 10.1016/j.mcpro.2023.100515

Authors:

Shahbazy et al.

Year:

2023

Dataset 1:

Short name	Immunopeptide spike
Repository ID	PXD034539
MS instrument	Orbitrap Fusion
Acquisition method	24 m/z wide-window DIA
Target sample	Immunopeptides isolated and purified from C1R-B*57:01 cells
Background sample	HeLa tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	Spike immunopeptides into HeLa background in 6 dilution ratios: 1, 0.8, 0.6, 0.4, 0.2, 0. Each sample is acquired for 3 replicates.
Additional runs	HLA-B*57:01 bound peptides are offline pre-fractionated into 9 fractions, and 9 DDA data are acquired.

mDIA BSA and HYE

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Reference:

[18]

Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel. 10.15252/msb.202211503

Authors:

Thielert et al.

Year:

2023

Dataset 1:

Short name	mDIA BSA
Repository ID	PXD038632
MS instrument	Orbitrap Exploris 480
Acquisition method	Variable wide-window DIA
Target sample	Tryptic digests of BSA
Background sample	/
PTM	/
Other sample	/
Brief design	Δ0/Δ4/Δ8 mix: 1) 17/2/1; 2) 7/2/1; 3) 5/3/2. Three replicates for each sample
Additional runs	/

Dataset 2:

Short name	mDIA HYE
Repository ID	PXD038632
MS instrument	timsTOF HT
Acquisition method	diaPASF / MS1-enhanced diaPASEF
Target sample	Tryptic digests of Yeast / E. coli
Background sample	Human tryptic digest
PTM	/
Other sample	/
Brief design	Δ0: HYE 65/15/20; Δ4: HYE 65/30/5; Δ8: HYE 65/5/30. Three replicates for each sample
Additional runs	/

UPS2 Orbi

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Reference:

[19]

Benchmarking DIA data analysis workflows. 10.1101/2023.06.02.543441

Authors:

Staes et al.

Year:

2023

Dataset 1:

Short name	UPS2 spike
Repository ID	/ (hasn’t been released in pre-print)
MS instrument	QE HF
Acquisition method	10 m/z inter-cycle overlapping-window DIA (5 m/z shift) (400-910 in odd-numbered cycle, 395-905 in even-numbered cycle, 1 MS1 scan every 30 MS2 scans)
Target sample	Tryptic UPS2
Background sample	Yeast tryptic digest
PTM	/
Other sample	Biognosys iRT peptides (C18)
Brief design	UPS2 + yeast background. Total 5 samples with UPS2 concentrations from 1x to 10x. 3 replicates.
Additional runs	1) Same UPS2 + yeast acquired by DDA (also 15 runs). 2) 3 pure UPS1 DDA runs and 3 pure UPS2 DDA runs.