TABLE 1.

Mass‐spectrometry based proteomic platforms used for identification and/or characterization of the differentially abundant proteins/modification sites in response to SARS‐CoV‐2 pathogenesis

Cell‐line/ tissue	Cell origin	Type of experiment	Proteomic platform	No. of Host proteins/ sites a	No of Virus Proteins/sites b	Reference
Cell lines
HuH7	Liver	Comparative	TMT, RPLC‐MS/MS	3562/‐	‐/‐	Appelberg et al., 2020[ 2 ]
Caco‐2	Colon	Comparative	TMT, LC‐MS/MS	412/‐	‐/‐	Bojkova et al., 2020[ 3 ]
Vero E6 #	Kidney	Comparative	SDS‐PAGE, LC‐MS/MS	1401/‐	‐/‐	Grenga et al., 2020[ 4 ]
Vero E6	Kidney	Comparative/ Targeted	LC‐MS/MS, TMT, DDA, Label Free, PRM	1499/‐	‐/‐	Zecha et al., 2020[ 5 ]
A549	Lung	Comparative	LC‐MS/MS, DIA, DDA	1053/‐	‐/‐	Stukalov et al., 2020[ 6 ]
A549	Lung	Immuno Proteomics	AP‐MS/MS,	1146/‐	‐/‐	Stukalov et al., 2020[ 6 ]
HEK293	Kidney	Immuno Proteomics	AP, LC‐MS/MS	295/‐	‐/‐	Li et al., 2020a[ 7 ]
HEK293	Kidney	Immuno Proteomics	BioID, LC‐MS/MS	2128/‐	‐/‐	Laurent et al., 2020[ 8 ]
HEK293	Kidney	Immuno Proteomics	BioID, LC‐MS/MS	1010/‐	‐/‐	St‐Germain et al., 2020[ 9 ]
HEK293T	Kidney	Immuno‐proteomic	AP, LC‐MS/MS	332/‐	‐/‐	Gordon et al., 2020[ 10 ]
A549	Lung	Immuno Proteomics	BioID, LC‐MS/MS	2242/‐	‐/‐	Samavarchi‐Tehrani et al., 2020[ 11 ]
HEK293T	Kidney	Immuno Proteomics	AP, TMT, LC‐MS/MS	51/‐	‐/‐	Davies et al., 2020[ 12 ]
iAT2	Lung	Comparative	TMT, LC‐MS/MS	2872/‐	‐/‐	Hekman et al., 2020[ 13 ]
Vero E6	Kidney	Shotgun/Targeted	LC‐HR‐MS/MS	‐/‐	6/‐	Gouveia et al., 2020a[ 14 ]
Vero E6	Kidney	Shotgun/Targeted	DDA, PRM, LC‐MS/MS	‐/‐	9/‐	Bezstarosti et al., 2020[ 15 ]
A549	Lung	Phospho Proteomics	EasyPhos, LC‐MS/MS,	‐/1483*	‐/‐	Stukalov et al., 2020[ 6 ]
A549	Lung	Ubiquitination	LC‐MS/MS	‐/884*	‐/‐	Stukalov et al., 2020[ 6 ]
Vero E6	Kidney	Phospho proteomics	LC‐MS/MS, label‐free	689/1524	5/25*	Bouhaddou et al., 2020[ 16 ]
iAT2	Lung	Phospho proteomics	TMT, LC‐MS/MS	1166/4688	2/11	Hekman et al., 2020[ 13 ]
Caco‐2	Colon	Phospho proteomics	TMT, LC‐SPS‐MS3, Fe‐NTA	‐/2996*	6/33	Klann et al., 2020[ 17 ]
Vero E6	Kidney	Phospho proteomics	SDS‐PAGE, TiO2, LC‐MS/MS	‐/‐	7/44*	Davidson et al., 2020[ 18 ]
Tissue
FFPE Tissues	Lung, Heart, Liver, spleen, Kidney, Testis, Thyroid	Comparative	TMT, LC‐MS/MS	5336/‐	‐/‐	Nie et al., 2021[ 19 ]
Lung	Lung	Comparative	LC‐MS/MS, label‐free	641/‐	‐/‐	Leng et al., 2020[ 20 ]
Liver	Liver	Comparative	LC‐MS/MS, label‐free	1043/‐	‐/‐	Leng et al., 2021[ 21 ]
Plasma	Blood	Comparative	nUHPLC‐MS/MS/DDA	91/‐	‐/‐	Park et al., 2020[ 22 ]
RBC	Blood	Comparative	nUHPLC‐MS/MS	78/‐	‐/‐	Thomas et al., 2020[ 23 ]
Serum	Blood	Comparative	TMT, UPLC‐MS/MS	105/‐	‐/‐	Shen et al., 2020[ 24 ]
Serum	Blood	Comparative	DIA/SWATH, LC‐MS/MS	35/‐	‐/‐	Messner et al., 2020[ 25 ]
PBMC	Blood	Comparative	TMT, LC‐MS/MS	726/‐	‐/‐	Li et al., 2020a[ 7 ]
Serum	Blood	Comparative	nUHPLC‐MS/MS	241/‐	‐/‐	D'Alessandro et al.,2020[ 26 ]
Saliva	Saliva	Immuno Proteomics	LC‐MS/MS	12/‐	‐/‐	Zhou and Wu, 2020[ 27 ]
Gargle solution	Saliva	Shotgun/Targeted	Nano‐HPLC/Nano‐ESI‐Orbitrap‐MS/MS	‐/‐	1/‐	Ihling et al., 2020[ 28 ]
Naso **	Nasal	Targeted	DDA, PRM, LC‐MS/MS	‐/‐	8/‐	Cardozo et al., 2020[ 29 ]
Naso	Nasal	Targeted	UPLC‐HR‐MS/MS, PRM	‐/‐	3/‐	Saadi et al., 2021[ 30 ]
Mucus	Lung	Targeted	UPLC‐HR‐MS/MS, PRM	‐/‐	2/‐	Cazares et al., 2020[ 31 ]
Naso	Nasal	Comparative	DIA LC‐MS/MS	17/‐	‐/‐	Akgun et al., 2020[ 32 ]
Naso	Nasal	Shotgun/Targeted	UPLC‐MS/MS	‐/‐	3/‐	Gouveia et al., 2020b[ 33 ]
Nasopharynx	Nasal	Shotgun/Targeted	UPLC‐MS/MS, PASEF	‐/‐	1/‐	Nikolaev et al., 2020[ 34 ]
Nasopharynx	Nasal	Shotgun/Targeted	LC‐MS/MS	‐/‐	2/‐	Schuster et al., 2020[ 35 ]
Extra Cellular
Urine	Urine	Comparative	LC‐MS/MS	322/‐	‐/‐	Li et al., 2020b[ 36 ]
Urine	Urine	Comparative	TIMS‐LC/MSMS, DIA	1986/‐	‐/‐	Tian et al., 2020[ 37 ]

**Naso‐oropharyngeal

^aNumber of significantly changed proteins/sites

^bNumber of proteins/sites identified

^#indicates non‐human cell‐line; N/A ‐ not applicable

*PTM sites/peptides; ‐ targeted proteomics/quantification.

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