CoronaMassKB Reanalyses

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Search Reanalyses: Filter Dataset Keywords: CoronaMassKB
Submitted MassIVE Reanalyses
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DatasetTitleDescriptionSpeciesDataset KeywordsConditionsBiological
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1
Differential analysis using MSstatsTMT and limma
RMSV000000308.3
Raw data were analyzed with Maestro and the PSM file was exported to R for the downstream statistical analysis. Data processing, protein quantification, and normalization steps were performed using MSstatsTMT v2.2.0. In total, 2,604 proteins were quantified and used for statistical analysis. Various statistical approaches, including MSstatsTMT and limma, are applied to detect changes in abundance In order to see how the unbalanced design impacted the performance of differential analysis, we manually generated an unbalanced design by eliminating a subset of samples from each mixture.
  • +Homo sapiens (NCBITaxon:9606)
  • +SARS-CoV-2
93000Ting Huang (huang704)
  • Q Exactive HF
  • +MOD:01720 - "A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-126 reporter+balance group."
Oct. 13, 2022, 12:14 AM00033179.11
2
  • A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Purposing
    MSV000085144 | PXD018117
Open modification searching of SARS-CoV-2-human protein interaction data with MSFragger
RMSV000000309.4 | RPXD018240.4
We performed a reanalysis of a SARS-CoV-2-human protein-protein interaction map from MSV000085144/PXD018117. With open modification searching (OMS) any type of PTM can be identified in an unbiased fashion, without the need to explicitly specify a limited number of variable modifications. This makes it possible to explore the general presence of PTMs in the context of the SARS-CoV-2 virus-host interactome. The reanalysis with ANN-SoLo (RMSV000000359.1) resulted in an over two-fold increase in identified spectra. Based on these identifications, our detected protein interactions showed a high overlap with independent mass spectrometry-based SARS-CoV-2 studies and virus-host interactions for alternative viruses, as well as previously unknown protein interactions. Additionally, we identified several novel modification sites on SARS-CoV-2 proteins that we investigated in relation to their interactions with host proteins. This reanalysis with MSFragger showed a decent overlap with the results from ANN-SoLo, illustrating that our results are not unique to ANN-SoLo and that a similar analysis could also be done with alternative OMS tools. In the original study affinity purification was performed using 27 SARS-CoV-2 proteins that were individually tagged and expressed in triplicate in HEK-293T cells. Bead-bound proteins were denatured, reduced, carbamidomethylated, and enzymatically digested using trypsin, and each sample was injected via an Easy-nLC 1200 (Thermo Fisher Scientific) into a Q-Exactive Plus mass spectrometer (Thermo Fisher Scientific). The SARS-CoV-2 proteins that were included are: all mature nonstructural proteins (Nsps), except for Nsp3 and Nsp16; a mutated version of Nsp5 to disable its proteolytic activity (Nsp5_C145A); and all predicted SARS-CoV-2 open reading frames (Orfs), including the spike (S), membrane (M), nucleocapsid (N), and envelope (E) protein. First, the downloaded raw files were converted to MGF files using ThermoRawFileParser (version 1.2.3). Next, OMS was performed using MSFragger (version 3.5) and FragPipe (version 18.0) against a concatenated FASTA file containing human protein sequences (Uniprot reviewed sequences downloaded on 2020/02/28), the SARS-CoV-2 protein sequences (version 2020/03/05), and the green fluorescent protein sequence. An equal number of decoy protein sequences were generated using FragPipe. The MSFragger search settings included a precursor mass tolerance between -150 Da and 500 Da, a fragment mass tolerance of 0.02 Da, and trypsin cleavage with up to two missed cleavages. Cysteine carbamidomethylation was used as a fixed modification, and oxidation of methionine and N-terminal acetylation were used as variable modifications. Other search settings were kept at their default values. PSMs were processed using PeptideProphet (version 4.4.0) with the FragPipe default settings for open searches and filtered at 1% FDR.
  • +Homo sapiens (NCBITaxon:9606)
  • +SARS-CoV-2
00000Charlotte Adams (CAdams)
  • Exactive Plus
  • MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset
Sep. 12, 2022, 6:20 AM0003172.44
3
  • A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Purposing
    MSV000085144 | PXD018117
Open modification searching of SARS-CoV-2-human protein interaction data reveals novel viral modification sites
RMSV000000359.1
We performed a reanalysis of a SARS-CoV-2-human protein-protein interaction map from MSV000085144/PXD018117. Open modification searching was used to investigate the presence of PTMs in the context of the SARS-CoV-2 virus-host PPI network. Based on an over two-fold increase in identified spectra, our detected protein interactions show a high overlap with independent mass spectrometry-based SARS-CoV-2 studies and virus-host interactions for alternative viruses, as well as previously unknown protein interactions. Additionally, we identified several novel modification sites on SARS-CoV-2 proteins that we investigated in relation to their interactions with host proteins. A detailed analysis of relevant modifications, including phosphorylation, ubiquitination, and S-nitrosylation, provides important hypotheses about the functional role of these modifications during viral infection by SARS-CoV-2. In the original study affinity purification was performed using 27 SARS-CoV-2 proteins that were individually tagged and expressed in triplicate in HEK-293T cells. Bead-bound proteins were denatured, reduced, carbamidomethylated, and enzymatically digested using trypsin, and each sample was injected via an Easy-nLC 1200 (Thermo Fisher Scientific) into a Q-Exactive Plus mass spectrometer (Thermo Fisher Scientific). The SARS-CoV-2 proteins that were included are: all mature nonstructural proteins (Nsps), except for Nsp3 and Nsp16; a mutated version of Nsp5 to disable its proteolytic activity (Nsp5_C145A); and all predicted SARS-CoV-2 open reading frames (Orfs), including the spike (S), membrane (M), nucleocapsid (N), and envelope (E) protein. First, the downloaded raw files were converted to MGF files using ThermoRawFileParser (version 1.2.3). Next, OMS was performed using the ANN-SoLo spectral library search engine (version 0.2.4). A combined human-SARS-CoV-2 spectral library was used for searching. The MassIVE-KB library (version 2018/06/15) was used as human spectral library. SARS-CoV-2 spectra were simulated by generating all possible tryptic peptide sequences from the SARS-CoV-2 protein sequences downloaded from UniProt (version 2020/03/05) using Pyteomics (version 4.3.2) and predicting the corresponding spectra using Prosit (version prosit_intensity_2020_hcd; collision energy 33 as determined by Prosit collision energy calibration). A simulated spectral library for the green fluorescent protein was generated in a similar fashion. A final spectral library was compiled by merging all spectra using SpectraST (version 5.0) and adding decoy spectra in a 1:1 ratio using the shuffle-and-reposition method. ANN-SoLo was configured to use a 20 ppm precursor mass tolerance during the first step of its cascade search and a 500 Da precursor mass tolerance during its open search. Other search settings were to filter peaks below 101 m/z, above 1500 m/z, and in a 0.5 m/z window around the precursor mass; a 0.02 m/z fragment mass tolerance; and a bin size of 0.05 m/z. The remaining settings were kept at their default values. Peptide-spectrum matches (PSMs) were filtered at 1% FDR.
  • +Homo sapiens (NCBITaxon:9606)
  • +SARS-CoV-2
00108,21400Charlotte Adams (CAdams)
  • Exactive Plus
  • MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset
Mar. 7, 2022, 1:28 PM830,74399,143108,21420114424.47
4
  • +
    Human Calu-3 cell proteome response to a wild type infectious clone of H7N9 and mutant H7N9 viruses
    MSV000079164 | PXD002385
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000080026, MSV000079164 / PXD002385, MSV000080025 / PXD004716 Calu-3 response to H1N1, H7N9 and MERS viral infection
RMSV000000320.2
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000080026, MSV000079164 / PXD002385, MSV000080025 / PXD004716 Calu-3 response to H1N1, H7N9 and MERS viral infection
  • +Homo sapiens (NCBITaxon:9606)
  • +omics
21693,7102,9122,342CCMS System (ccms)
  • +LTQ Orbitrap
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 30, 2021, 10:59 AM3,496,46633,110108,6221517581.92
5
  • A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Purposing
    MSV000085144 | PXD018117
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000085144 / PXD018117 A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Purposing
RMSV000000316.3
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000085144 / PXD018117 A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Purposing
  • +Homo sapiens (NCBITaxon:9606)
  • +SARS-CoV-2
31952,70529,6794,410CCMS System (ccms)
  • Exactive Plus
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 7:19 PM766,39832,52987,511428852.38
6
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on MS-GF+ reanalysis of MSV000085494 / PXD018357 Inhibition of growth factor signaling prevents SARS-CoV-2 replication, Non-phospho files only
RMSV000000341.4 | RPXD025723.4
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on MS-GF+ reanalysis of MSV000085494 / PXD018357 Inhibition of growth factor signaling prevents SARS-CoV-2 replication, Non-phospho files only
  • +Homo sapiens (NCBITaxon:9606)
  • +TMT
216,8156,6764,019CCMS System (ccms)
  • Orbitrap Fusion Lumos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 7:00 PM145,43877,953104,93812411.13
7
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on MS-GF+ reanalysis of MSV000085494 / PXD018357 Inhibition of growth factor signaling prevents SARS-CoV-2 replication, Phospho files only
RMSV000000341.3 | RPXD025723.3
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on MS-GF+ reanalysis of MSV000085494 / PXD018357 Inhibition of growth factor signaling prevents SARS-CoV-2 replication, Phospho files only
  • +Homo sapiens (NCBITaxon:9606)
  • +TMT
213,6113,5052,695CCMS System (ccms)
  • Orbitrap Fusion Lumos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 6:53 PM42,15912,21721,66412152.64
8
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000079701 / PXD004100, MSV000080028 / PXD004718, MSV000081887 Primary human fibroblasts proteome response to an icMERS coronavirus
RMSV000000321.3
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000079701 / PXD004100, MSV000080028 / PXD004718, MSV000081887 Primary human fibroblasts proteome response to an icMERS coronavirus
  • +Homo sapiens (NCBITaxon:9606)
  • +omics
101483,1662,827121CCMS System (ccms)
  • LTQ Orbitrap Velos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 6:46 PM1,003,54630,81088,6211311436.10
9
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000085516 / PXD018970 Urine proteomics profiling of the COVID-19
RMSV000000343.1 | RPXD025724.1
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MSStats on Maestro/ MaxQuant reanalysis of MSV000085516 / PXD018970 Urine proteomics profiling of the COVID-19
  • +Homo sapiens (NCBITaxon:9606)
  • +Urine proteomics
4402,5432,232902CCMS System (ccms)
  • Orbitrap Fusion Lumos
  • +UNIMOD:4 - "Iodoacetamide derivative."
Apr. 29, 2021, 6:35 PM1,183,41941,198101,812139415.13
10
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro reanalysis of MSV000085494 / PXD018357 Inhibition of growth factor signaling prevents SARS-CoV-2 replication (Non-phospho files only)
RMSV000000341.2 | RPXD025723.2
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on Maestro reanalysis of MSV000085494 / PXD018357 Inhibition of growth factor signaling prevents SARS-CoV-2 replication (Non-phospho files only)
  • +Homo sapiens (NCBITaxon:9606)
  • +TMT
246,5756,4573,468CCMS System (ccms)
  • Orbitrap Fusion Lumos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 6:16 PM165,20566,353100,781137760.01
11
  • +
    Primary human microvascular endothelial cells proteome response to an icMERS coronavirus
    MSV000079703 | PXD004101
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000079703 / PXD004101, MSV000080029 / PXD004719, MSV000081888 Primary human microvascular endothelial cells Proteome response to an icMERS coronavirus
RMSV000000322.3
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000079703 / PXD004101, MSV000080029 / PXD004719, MSV000081888 Primary human microvascular endothelial cells Proteome response to an icMERS coronavirus
  • +Homo sapiens (NCBITaxon:9606)
  • +omics
101503,1742,8591,434CCMS System (ccms)
  • LTQ Orbitrap Velos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 6:06 PM1,870,96029,92085,9681412727.38
12
  • +
    GNPS - Primary human airway epithelial cells proteome response to an icMERS coronavirus
    MSV000083529
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000083529, MSV000083530, MSV000083531 Primary human airway epithelial cells proteome response to an icMERS coronavirus
RMSV000000342.1
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000083529, MSV000083530, MSV000083531 Primary human airway epithelial cells proteome response to an icMERS coronavirus
  • +Homo sapiens (NCBITaxon:9606)
  • +omics
101503,7313,475291CCMS System (ccms)
  • LTQ Orbitrap Velos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 5:20 PM3,697,34333,76065,3221416417.94
13
  • Human Calu-3 cell proteome response to Middle Eastern Respiratory Syndrome (icMERS) coronavirus
    MSV000080025 | PXD004716
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro /MaxQuant reanalysis of MSV000080025 / PXD004716 Human Calu-3 cell proteome response to Middle Eastern Respiratory Syndrome (icMERS) coronavirus
RMSV000000319.3
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on Maestro /MaxQuant reanalysis of MSV000080025 / PXD004716 Human Calu-3 cell proteome response to Middle Eastern Respiratory Syndrome (icMERS) coronavirus
  • +Homo sapiens (NCBITaxon:9606)
  • +omics
36302,7132,510332CCMS System (ccms)
  • LTQ Orbitrap
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 5:02 PM648,16622,07748,2961410760.24
14
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000080026 Calu-3 cell proteome response to H1N1 virus
RMSV000000317.3
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on Maestro/MaxQuant reanalysis of MSV000080026 Calu-3 cell proteome response to H1N1 virus
  • +Homo sapiens (NCBITaxon:9606)
  • +omics
12642,2092,03683CCMS System (ccms)
  • LTQ Orbitrap
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 3:52 PM432,77018,21441,696159355.84
15
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000085510 / PXD018594 Shotgun proteomics of Vero E6 cells infected by Italy-INMI1 SARS-CoV-2 virus
RMSV000000340.1 | RPXD025722.1
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000085510 / PXD018594 Shotgun proteomics of Vero E6 cells infected by Italy-INMI1 SARS-CoV-2 virus
  • +Betacoronavirus sp. (NCBITaxon:1928434)
  • +coronavirus
221,8821,6221,008CCMS System (ccms)
  • Q Exactive HF
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 3:35 PM930,91914,03623,319149197.30
16
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro reanalysis of MSV000085507 / PXD019221 Proteomic and Metabolomic Characterization of COVID-19 Patient Sera
RMSV000000331.3
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on Maestro reanalysis of MSV000085507 / PXD019221 Proteomic and Metabolomic Characterization of COVID-19 Patient Sera
  • +Homo sapiens (NCBITaxon:9606)
  • +COVID-19
591335371205CCMS System (ccms)
  • Q Exactive HF
  • +UNIMOD:4 - "Iodoacetamide derivative."
Apr. 28, 2021, 11:33 PM1,339,85420,141135,2571310219.80
17
CoronaMassKB hackathon: MassIVE/CCMS MSStats on Maestro reanalysis of MSV000085349 / PXD018581 Proteomics of SARS-CoV and SARS-CoV-2 infected cells, Non-phospho files only
RMSV000000313.4
CoronaMassKB hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on Maestro reanalysis of MSV000085349 / PXD018581 Proteomics of SARS-CoV and SARS-CoV-2 infected cells
  • +Homo sapiens (NCBITaxon:9606)
  • +COVID19
968,4218,1205,609CCMS System (ccms)
  • Q Exactive HF-X
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 28, 2021, 10:52 PM540,238158,104318,931148609.50
18
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro reanalysis of MSV000085494 / PXD018357 Inhibition of growth factor signaling prevents SARS-CoV-2 replication (Phospho files only)
RMSV000000341.1 | RPXD025723.1
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on Maestro reanalysis of MSV000085494 / PXD018357 Inhibition of growth factor signaling prevents SARS-CoV-2 replication (Phospho files only)
  • +Homo sapiens (NCBITaxon:9606)
  • +TMT
243,1273,0552,253CCMS System (ccms)
  • Orbitrap Fusion Lumos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 28, 2021, 10:32 PM77,82114,75829,455137609.17
19
  • A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Purposing
    MSV000085144 | PXD018117
Illustrated end-to-end PPI reanalysis
RMSV000000309.3 | RPXD018240.3
Identification results for the end-to-end PPI reanalysis described in the following Jupyter notebook: https://github.com/bittremieux/sars_cov_2
  • +Homo sapiens (NCBITaxon:9606)
  • +SARS-CoV-2
001,81300Wout Bittremieux (woutb)
  • MS:1002526
  • MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset
Nov. 5, 2020, 6:06 PM173,74813,10216,096584.52
20
  • A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Purposing
    MSV000085144 | PXD018117
Illustrated end-to-end PPI reanalysis
RMSV000000309.2 | RPXD018240.2
Identification results for the end-to-end PPI reanalysis described in the following Jupyter notebook: https://github.com/bittremieux/sars_cov_2
  • +Homo sapiens (NCBITaxon:9606)
  • +SARS-CoV-2
00000Wout Bittremieux (woutb)
  • MS:1002526
  • MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset
Sep. 29, 2020, 1:54 PM000102382.15
21
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on MS-GF+ reanalysis of MSV000085507 / PXD019221 Proteomic and Metabolomic Characterization of COVID-19 Patient Sera
RMSV000000331.2
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSStats on MS-GF+ reanalysis of MSV000085507 / PXD019221 Proteomic and Metabolomic Characterization of COVID-19 Patient Sera
  • +Homo sapiens (NCBITaxon:9606)
  • +COVID-19
55640605305CCMS System (ccms)
  • Q Exactive HF
  • +UNIMOD:4 - "Iodoacetamide derivative."
Jul. 2, 2020, 2:44 PM261,9847,71215,65012757.25
22
CoronaMassKB Hackathon: MassIVE/CCMS Maestro reanalysis of MSV000085507 / PXD019221 Proteomic and Metabolomic Characterization of COVID-19 Patient Sera
RMSV000000331.1
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS Maestro reanalysis of MSV000085507 / PXD019221 Proteomic and Metabolomic Characterization of COVID-19 Patient Sera
  • +Homo sapiens (NCBITaxon:9606)
  • +COVID-19
0033500Nuno Bandeira (nuno)
  • Q Exactive HF
  • +UNIMOD:4 - "Iodoacetamide derivative."
Jul. 2, 2020, 1:08 PM1,339,85420,141135,25742323.04
23
MassIVE.quant reanalysis from the original manuscript
RMSV000000327.3 | RPXD019844.3
This reanalysis is the statistical analysis results from the original manuscript. The raw spectra were analyzed by Proteome Discoverer 2.4.1.15. The protein report includes peptide abundance, protein abundance, and significant statistical testing results which were measured on the training cohort (17 replicates from 17 Healthy patients, 19 replicates from 18 non-COVID-19 patients, 20 replicates from 18 non-severe COVID-19 patients and 14 replicates from 13 severe COVID-19 patients). Log2 fold change (log2 FC) was calculated on the mean of the same patient group for each pair of comparing groups. Two-sided unpaired Welch's t-test was performed for each pair of comparing groups and adjusted p values were calculated using Benjamini & Hochberg correction.
  • +Homo sapiens (NCBITaxon:9606)
  • +COVID-19
000134134Ting Huang (huang704)
  • Q Exactive HF
  • +UNIMOD:4 - "Iodoacetamide derivative."
Jun. 17, 2020, 12:26 PM000843841.73
24
MassIVE.quant reanalysis from offline PD+MSstatsTMT results
RMSV000000327.2 | RPXD019844.2
The same PSM report from Proteome Discoverer 2.4.1.15 (Thermo Fisher Scientific) in RMSV000000327.3 was used for this reanalysis. For statistical analysis, data preprocessing, multiple fractions combination, data normalization with reference channel, protein summarization, and statistical testing using MSstatsTMT v1.6.2 was performed. The PSM report measures the training cohort described in the original manuscript, which includes 17 replicates from 17 Healthy patients, 19 replicates from 18 non-COVID-19 patients, 20 replicates from 18 non-severe COVID-19 patients and 14 replicates from 13 severe COVID-19 patients. The remaining 20 replicates are not used for this reanalysis and thus were labeled as "Empty" condition. R script for MSstatsTMT analysis is available in the 'methods' folder (FTP download -> methods).
  • +Homo sapiens (NCBITaxon:9606)
  • +COVID-19
5670786339Ting Huang (huang704)
  • Q Exactive HF
  • +UNIMOD:4 - "Iodoacetamide derivative."
Jun. 17, 2020, 10:21 AM0001844012.65
25
  • +
    Primary human microvascular endothelial cells proteome response to an icMERS coronavirus
    MSV000079703 | PXD004101
CoronaMassKB Hackathon: MassIVE/CCMS MSGF+ reanalysis of MSV000079703 / PXD004101, MSV000080029 / PXD004719, MSV000081888 Primary human microvascular endothelial cells Proteome response to an icMERS coronavirus
RMSV000000322.2
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSGF+ reanalysis of MSV000079703 / PXD004101, MSV000080029 / PXD004719, MSV000081888 Primary human microvascular endothelial cells Proteome response to an icMERS coronavirus
  • +Homo sapiens (NCBITaxon:9606)
  • +omics
101503,49500CCMS System (ccms)
  • LTQ Orbitrap Velos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Jun. 3, 2020, 11:15 PM1,401,85229,28262,573123170.69
26
CoronaMassKB Hackathon: MassIVE/CCMS MSGF+ reanalysis of MSV000079701 / PXD004100, MSV000080028 / PXD004718, MSV000081887 Primary human fibroblasts proteome response to an icMERS coronavirus
RMSV000000321.2
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSGF+ reanalysis of MSV000079701 / PXD004100, MSV000080028 / PXD004718, MSV000081887 Primary human fibroblasts proteome response to an icMERS coronavirus
  • +Homo sapiens (NCBITaxon:9606)
  • +omics
101483,63300CCMS System (ccms)
  • LTQ Orbitrap Velos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Jun. 3, 2020, 11:04 PM1,622,33632,72570,226123753.23
27
  • Human Calu-3 cell proteome response to Middle Eastern Respiratory Syndrome (icMERS) coronavirus
    MSV000080025 | PXD004716
CoronaMassKB Hackathon: MassIVE/CCMS MSGF+ reanalysis of MSV000080025 / PXD004716 Human Calu-3 cell proteome response to Middle Eastern Respiratory Syndrome (icMERS) coronavirus
RMSV000000319.2
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSGF+ reanalysis of MSV000080025 / PXD004716 Human Calu-3 cell proteome response to Middle Eastern Respiratory Syndrome (icMERS) coronavirus
  • +Homo sapiens (NCBITaxon:9606)
  • +omics
36302,53900CCMS System (ccms)
  • LTQ Orbitrap
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Jun. 3, 2020, 10:51 PM989,02619,51236,80582267.32
28
CoronaMassKB Hackathon: MassIVE/CCMS MSGF+ reanalysis of MSV000080026 Calu-3 cell proteome response to H1N1 virus
RMSV000000317.2
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSGF+ reanalysis of MSV000080026 Calu-3 cell proteome response to H1N1 virus
  • +Homo sapiens (NCBITaxon:9606)
  • +omics
12641,89000CCMS System (ccms)
  • LTQ Orbitrap
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Jun. 3, 2020, 10:45 PM311,93413,95924,54310754.74
29
  • A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Purposing
    MSV000085144 | PXD018117
CoronaMassKB Hackathon: MassIVE/CCMS MSGF+ reanalysis of MSV000085144 / PXD018117 A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Purposing
RMSV000000316.2
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSGF+ reanalysis of MSV000085144 / PXD018117 A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Purposing
  • +Homo sapiens (NCBITaxon:9606)
  • +SARS-CoV-2
31953,35900CCMS System (ccms)
  • MS:1002526
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Jun. 3, 2020, 10:33 PM472,19433,39655,24410993.89
30
CoronaMassKB Hackathon: MassIVE/CCMS MSGF+ reanalysis of MSV000085096 / PXD017710 Proteome and Translatome of SARS-CoV-2 infected cells
RMSV000000315.2
CoronaMassKB Hackathon: Early-access community reanalysis of mass spectrometry data. MassIVE/CCMS MSGF+ reanalysis of MSV000085096 / PXD017710 Proteome and Translatome of SARS-CoV-2 infected cells
  • +Homo sapiens (NCBITaxon:9606)
  • +SARS-CoV-2
1037,16900CCMS System (ccms)
  • Q Exactive HF
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Jun. 3, 2020, 10:29 PM504,88484,232163,22891339.84