Table 1.
Compilation of recent research using proteomic approaches in a SARS-CoV-2 context.
| Objective | Authors | Sample | Technological platform | Findings |
|---|---|---|---|---|
| SARS-CoV-2 interactome | Liang et al. (2020) | SARS-CoV-2 proteins and HEK293 cells | LC-MS/MS (Q-Exactive Orbitrap) | Identification of 332 high-confidence SARS-CoV-2 human PPIs; 62 of them have drugs/preclinical molecules that modulate them |
| Gordon et al. (2020) | SARS-CoV-2 proteins and HEK293 cells | LC-MS/MS (Q-Exactive Plus) | Identification of 631 SARS-CoV-2 human PPIs (deregulation in translation, degradation, inflammatory, and innate immune system) | |
| Stukalov et al. (2020) | SARS-CoV-2 proteins and A549 cells | LC-MS/MS (Q-Exactive HF-X) | Identification of 1,484 interactions between 1,086 cellular proteins and 24 SARS-CoV-2 targets involving innate immunity and stress response components, and DNA damage response mediators | |
| SARS-CoV-2 in vitro models | Bojkova et al. (2020) | Caco-212 cells (colon) | LC-MS/MS (Q-Exactive HF) | Proteins |
| Grenga et al. (2020) | Vero cells (renal) | LC-MS/MS (Q-Exactive HF) | Alteration in membrane trafficking, pre-processing in ER and regulation of mRNA processing/splicing via spliceosome | |
| Davidson et al. (2020) | Vero cells (renal) | RNAseq + LC-MS/MS (Q-Exactive HF) | Identification of an 8 amino acid deletion in the S glycoprotein that potentially affects protein cleavage, cell tropism, and infectivity | |
| Appelberg et al. (2020) | HuH7 cells (hepatic) | RNAseq + LC-MS/MS (Orbitrap Fusion Lumos) | Proteo-transcriptomic analysis has identified disruptions in ErbB, HIF-1, mTOR, and TNF signaling | |
| Covid-19 pathology study and diagnosis | Ihling et al. (2020) | Gargle | LC-MS/MS (Orbitrap-HCD) | An MS method that specifically detects unique peptides from SARS-CoV-2 nucleoprotein from gargle samples |
| Bezstarosti et al. (2020) | Vero cells (renal) | LC-MS/MS (Orbitrap Eclipse Tribrid) | A parallel reaction monitoring approach to detect the SARS-CoV-2 nucleocapsid protein in the mid-attomole range | |
| Nikolaev et al. (2020) | Nasopharynx | LC-MS/MS (TIMS-TOF) | Confident identification of the SARS-CoV-2 N protein in patients with low viral load | |
| Wang et al. (2020) | Serum | Microarray (n.d.) | Antibodies commercially available for SARS-CoV-1 proteins can also target SARS-CoV-2 proteins | |
| Zhang et al. (2020) | Serum | Microarray (GenePix 4300A microarray) | The S protein S1-RBD might be the optimal antigen for IgM antibody detection, while the S protein extracellular domain would be the optimal antigen for both IgM and IgG antibody detection | |
| Shen et al. (2020) | Serum | LC-MS/MS (Q-Exactive HF-X) | Deregulation of 93 proteins and 204 metabolites revealed metabolic and immune dysregulation in patients with COVID-19 | |
| Liang et al. (2020) | PBMCs | LC-MS/MS (Q-Exactive Orbitrap) | Two hundred and twenty differential expressed proteins involved in neutrophil chemotaxis, type I interferon signaling pathway, inflammatory response, and antigen processing and presentation in PBMCs from patients with COVID-19 | |
| Messner et al. (2020) | Serum | LC-MS/MS (TripleTOF 6600) | Twenty-seven potential serum biomarkers that distinguish mild and severe forms of COVID-19 | |
| Akgun et al. (2020) | Nasopharyngeal swab | LC-MS/MS [Xevo G2-XS QTOF (SONAR)] | Seventeen differentially expressed proteins across COVID-19 samples involved in neutrophil degranulation and innate immune responses | |
| Liang et al. (2020) | Urine | LC-MS/MS (Orbitrap Fusion Lumos) | A severe proteomic imbalance among COVID-19 samples with an impact on immune response, complement activation, platelet degranulation, lipoprotein metabolic process, and response to hypoxia |
ER, endoplasmic reticulum; ErbB, epidermal growth factor receptor; HIF-1, hypoxia-inducible factor 1; IgG, immunoglobulin G; IgM, immunoglobulin M; LC-MS/MS, liquid chromatography with tandem mass spectrometry; mTOR, mammalian target of rapamycin; n.d., not determined; PBMC, peripheral blood mononuclear cell; PPI, protein-protein interaction; S1-RBD, subunit 1 receptor binding domain; TIMS-TOF, trapped ion mobility spectrometry-time of flight; TNF, tumor necrosis factor.