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Spike-in benchmark study : Ubiquitination, Label-free experimentsMSV000088971
MSstatsPTM Analysis of Spike-in benchmark study with comparison to limma and ANOVARMSV000000669.1
MSstatsPTM analysis of Spike-in benchmark study. Includes all code and intermediate data to reprocess results. Includes comparisons with other methods including limma and ANOVA.
MassIVE/CCMS MSStats on Maestro /MaxQuant reanalysis of MSV000082204 / PXD005940 Global Proteome Analysis of the NCI-60 Cell Line PanelRMSV000000631.1 | RPXD033211.1
MassIVE/CCMS MSStats on Maestro /MaxQuant reanalysis of MSV000082204 / PXD005940 Global Proteome Analysis of the NCI-60 Cell Line Panel
MassIVE/CCMS MSStats on Maestro reanalysis of MSV000086387 / PXD016999 A Quantitative Proteome Map of the Human BodyRMSV000000635.1 | RPXD033216.1
MassIVE/CCMS MSStats on Maestro reanalysis of MSV000086387 / PXD016999 A Quantitative Proteome Map of the Human Body
Proteomics
Homo sapiens (NCBITaxon:9606)
33
56
2
9,154
8,913
115
11297.20
CCMS System (ccms)
Orbitrap Fusion
+UNIMOD:4 - "Iodoacetamide derivative."
UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:1 - "Acetylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:5 - "Carbamylation."
UNIMOD:7 - "Deamidation."
UNIMOD:737 - "Sixplex Tandem Mass Tag."
Apr. 13, 2022, 12:57 PM
5,480,723
208,696
489,490
13,465
4
Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumorsMSV000085343 | PXD014414
MassIVE/CCMS MSStats on Maestro reanalysis of MSV000085343 / PXD014414 Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumorsRMSV000000630.1 | RPXD033210.1
MassIVE/CCMS MSStats on Maestro reanalysis of MSV000085343 / PXD014414 Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors
Proteomics
+Homo sapiens (NCBITaxon:9606)
Mus musculus (NCBITaxon:10090)
3
27
1
4,604
86
11
1231.44
CCMS System (ccms)
Orbitrap Fusion
+UNIMOD:4 - "Iodoacetamide derivative."
UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:1 - "Acetylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:5 - "Carbamylation."
UNIMOD:7 - "Deamidation."
UNIMOD:737 - "Sixplex Tandem Mass Tag."
Apr. 13, 2022, 12:14 PM
249,276
38,586
57,872
4,675
5
Shigella Ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infectionMSV000088966
MSstatsPTM Analysis of Shigella Ubiquitin ligase IpaH7.8 ExperimentRMSV000000356.1
MSstatsPTM Analysis of the Shigella Ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infection experiment (MSV000088966). Includes input, quantification, and statistical analysis results for both KGG and global protein (unmodified) measurements.
+TMT
Global proteome
ubiquitylome
Homo sapiens (NCBITaxon:9606)
0
0
0
16,969
6,580
10
207.29
Devon Kohler (devonjkohler)
Orbitrap Fusion Lumos
+MOD:01060 - "A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine."
UNIMOD:737 - "Sixplex Tandem Mass Tag."
MOD:01722 - "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Proteome Sciences TMT6plex-126 reporter+balance group."
MOD:01723 - "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Proteome Sciences TMT6plex-126 reporter+balance group."
Mar. 7, 2022, 7:57 AM
0
0
0
0
6
SWATH Analysis of Yeast Proteome over Time in Response to Osmotic StressMSV000081677 | PXD001010
this is the result using MSstats during May Institute 2021 week2 hands-on session.
+yeast
SWATH-MS
5600
osmotic stress
Saccharomyces cerevisiae (NCBITaxon:4932)
6
3
1
2,069
810
9
198.91
Meena Choi (mnchoi)
+TripleTOF 5600
TSQ Quantum
+00935
01060
May. 13, 2021, 11:08 AM
0
0
0
0
7
+
Human Calu-3 cell proteome response to a wild type infectious clone of H7N9 and mutant H7N9 viruses MSV000079164 | PXD002385
Human Calu-3 cell proteome response to Middle Eastern Respiratory Syndrome (icMERS) coronavirusMSV000080025 | PXD004716
Calu-3 cell proteome response to H1N1 virusMSV000080026
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000080026, MSV000079164 / PXD002385, MSV000080025 / PXD004716 Calu-3 response to H1N1, H7N9 and MERS viral infectionRMSV000000320.2
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
+omics
proteomics
MERS-CoV
CoronaMassKB
H7N9
H1N1
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Middle East respiratory syndrome-related coronavirus (NCBITaxon:1335626)
Influenza A virus (A/Wilson-Smith/1933(H1N1)) (NCBITaxon:381518)
2
169
4
2,912
2,342
15
17581.92
CCMS System (ccms)
+LTQ Orbitrap
LTQ Orbitrap Velos
+UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:5 - "Carbamylation."
UNIMOD:1 - "Acetylation."
UNIMOD:7 - "Deamidation."
UNIMOD:4 - "Iodoacetamide derivative."
Apr. 30, 2021, 10:59 AM
3,496,466
33,110
108,622
3,710
8
A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-PurposingMSV000085144 | 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-PurposingRMSV000000316.3
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
+SARS-CoV-2
coronavirus
COVID-19
PPI
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Severe acute respiratory syndrome coronavirus 2 (NCBITaxon:2697049)
31
95
1
29,679
4,410
42
8852.38
CCMS System (ccms)
Exactive Plus
+UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:5 - "Carbamylation."
UNIMOD:1 - "Acetylation."
UNIMOD:7 - "Deamidation."
Apr. 29, 2021, 7:19 PM
766,398
32,529
87,511
2,705
9
Inhibition of growth factor signaling prevents SARS-CoV-2 replicationMSV000085494 | PXD018357
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 onlyRMSV000000341.4 | 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
+TMT
SARS-CoV-2
COVID-19
Infection
Phospho
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Severe acute respiratory syndrome coronavirus 2 (NCBITaxon:2697049)
2
1
5
6,676
4,019
12
411.13
CCMS System (ccms)
Orbitrap Fusion Lumos
+UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:21 - "Phosphorylation."
UNIMOD:5 - "Carbamylation."
UNIMOD:1 - "Acetylation."
UNIMOD:7 - "Deamidation."
UNIMOD:737 - "Sixplex Tandem Mass Tag."
UNIMOD:4 - "Iodoacetamide derivative."
Apr. 29, 2021, 7:00 PM
145,438
77,953
104,938
6,815
10
Inhibition of growth factor signaling prevents SARS-CoV-2 replicationMSV000085494 | PXD018357
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on MS-GF+ reanalysis of MSV000085494 / PXD018357 Inhibition of growth factor signaling prevents SARS-CoV-2 replication, Phospho files onlyRMSV000000341.3 | 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
+TMT
SARS-CoV-2
COVID-19
Infection
Phospho
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Severe acute respiratory syndrome coronavirus 2 (NCBITaxon:2697049)
2
1
5
3,505
2,695
12
152.64
CCMS System (ccms)
Orbitrap Fusion Lumos
+UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:21 - "Phosphorylation."
UNIMOD:5 - "Carbamylation."
UNIMOD:1 - "Acetylation."
UNIMOD:7 - "Deamidation."
UNIMOD:737 - "Sixplex Tandem Mass Tag."
UNIMOD:4 - "Iodoacetamide derivative."
Apr. 29, 2021, 6:53 PM
42,159
12,217
21,664
3,611
11
+
Primary human fibroblasts proteome response to an icMERS coronavirusMSV000079701 | PXD004100
Primary human fibroblasts proteome response to an icMERS coronavirusMSV000080028 | PXD004718
Primary human fibroblasts Proteome response to an icMERS coronavirusMSV000081887
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000079701 / PXD004100, MSV000080028 / PXD004718, MSV000081887 Primary human fibroblasts proteome response to an icMERS coronavirusRMSV000000321.3
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
+omics
proteomics
MERS-CoV
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Middle East respiratory syndrome-related coronavirus (NCBITaxon:1335626)
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000085516 / PXD018970 Urine proteomics profiling of the COVID-19RMSV000000343.1 | 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
+Urine proteomics
COVID-19
SARS-CoV-2
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Severe acute respiratory syndrome coronavirus 2 (NCBITaxon:2697049)
4
40
3
2,232
902
13
9415.13
CCMS System (ccms)
Orbitrap Fusion Lumos
+UNIMOD:4 - "Iodoacetamide derivative."
UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:5 - "Carbamylation."
UNIMOD:1 - "Acetylation."
UNIMOD:7 - "Deamidation."
Apr. 29, 2021, 6:35 PM
1,183,419
41,198
101,812
2,543
13
Inhibition of growth factor signaling prevents SARS-CoV-2 replicationMSV000085494 | PXD018357
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)
+TMT
SARS-CoV-2
COVID-19
Infection
Phospho
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Severe acute respiratory syndrome coronavirus 2 (NCBITaxon:2697049)
2
4
5
6,457
3,468
13
7760.01
CCMS System (ccms)
Orbitrap Fusion Lumos
+UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:5 - "Carbamylation."
UNIMOD:1 - "Acetylation."
UNIMOD:7 - "Deamidation."
UNIMOD:737 - "Sixplex Tandem Mass Tag."
UNIMOD:4 - "Iodoacetamide derivative."
Apr. 29, 2021, 6:16 PM
165,205
66,353
100,781
6,575
14
+
Primary human microvascular endothelial cells proteome response to an icMERS coronavirusMSV000079703 | PXD004101
Primary human microvascular endothelial cells proteome response to an icMERS coronavirusMSV000080029 | PXD004719
Primary human microvascular endothelial cells Proteome response to an icMERS coronavirusMSV000081888
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 coronavirusRMSV000000322.3
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
+omics
proteomics
MERS-CoV
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Middle East respiratory syndrome-related coronavirus (NCBITaxon:1335626)
10
150
1
2,859
1,434
14
12727.38
CCMS System (ccms)
LTQ Orbitrap Velos
+UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:5 - "Carbamylation."
UNIMOD:1 - "Acetylation."
UNIMOD:7 - "Deamidation."
UNIMOD:4 - "Iodoacetamide derivative."
Apr. 29, 2021, 6:06 PM
1,870,960
29,920
85,968
3,174
15
+
GNPS - Primary human airway epithelial cells proteome response to an icMERS coronavirusMSV000083529
GNPS - Primary human airway epithelial cells proteome response to an icMERS coronavirusMSV000083530
GNPS - Primary human airway epithelial cells proteome response to an icMERS coronavirusMSV000083531
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000083529, MSV000083530, MSV000083531 Primary human airway epithelial cells proteome response to an icMERS coronavirusRMSV000000342.1
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
+omics
proteomics
MERS-CoV
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Middle East respiratory syndrome-related coronavirus (NCBITaxon:1335626)
10
150
1
3,475
291
14
16417.94
CCMS System (ccms)
LTQ Orbitrap Velos
+UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:5 - "Carbamylation."
UNIMOD:1 - "Acetylation."
UNIMOD:7 - "Deamidation."
UNIMOD:4 - "Iodoacetamide derivative."
Apr. 29, 2021, 5:20 PM
3,697,343
33,760
65,322
3,731
16
Human Calu-3 cell proteome response to Middle Eastern Respiratory Syndrome (icMERS) coronavirusMSV000080025 | 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) coronavirusRMSV000000319.3
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
+omics
proteomics
MERS-CoV
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Middle East respiratory syndrome-related coronavirus (NCBITaxon:1335626)
36
30
1
2,510
332
14
10760.24
CCMS System (ccms)
LTQ Orbitrap
+UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:5 - "Carbamylation."
UNIMOD:1 - "Acetylation."
UNIMOD:7 - "Deamidation."
Apr. 29, 2021, 5:02 PM
648,166
22,077
48,296
2,713
17
Calu-3 cell proteome response to H1N1 virusMSV000080026
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro/ MaxQuant reanalysis of MSV000080026 Calu-3 cell proteome response to H1N1 virusRMSV000000317.3
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
+omics
proteomics
H1N1
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Influenza A virus (A/Wilson-Smith/1933(H1N1)) (NCBITaxon:381518)
12
64
1
2,036
83
15
9355.84
CCMS System (ccms)
LTQ Orbitrap
+UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:5 - "Carbamylation."
UNIMOD:1 - "Acetylation."
UNIMOD:7 - "Deamidation."
Apr. 29, 2021, 3:52 PM
432,770
18,214
41,696
2,209
18
Shotgun proteomics of Vero E6 cells infected by Italy-INMI1 SARS-CoV-2 virusMSV000085510 | PXD018594
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 virusRMSV000000340.1 | 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
+coronavirus
SARS-CoV-2
COVID-19
virus
kinetics
viral particle
host response
severe acute respiratory syndrome
vaccine
CoronaMassKB
ProteoCarta
+Betacoronavirus sp. (NCBITaxon:1928434)
Chlorocebus aethiops aethiops (NCBITaxon:101841)
Severe acute respiratory syndrome coronavirus 2 (NCBITaxon:2697049)
2
2
10
1,622
1,008
14
9197.30
CCMS System (ccms)
Q Exactive HF
+UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:5 - "Carbamylation."
UNIMOD:1 - "Acetylation."
UNIMOD:7 - "Deamidation."
Apr. 29, 2021, 3:35 PM
930,919
14,036
23,319
1,882
19
GNPS - Proteomic and Metabolomic Characterization of COVID-19 Patient SeraMSV000085507 | PXD019221
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on Maestro reanalysis of MSV000085507 / PXD019221 Proteomic and Metabolomic Characterization of COVID-19 Patient SeraRMSV000000331.3
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
+COVID-19
Proteomics
Metabolomics
Severity
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Severe acute respiratory syndrome coronavirus 2 (NCBITaxon:2697049)
CoronaMassKB hackathon: MassIVE/CCMS MSStats on Maestro reanalysis of MSV000085349 / PXD018581 Proteomics of SARS-CoV and SARS-CoV-2 infected cells, Non-phospho files onlyRMSV000000313.4
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
+COVID19
SARS-CoV
SARS-CoV-2
TMT
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Severe acute respiratory syndrome-related coronavirus (NCBITaxon:694009)
Severe acute respiratory syndrome coronavirus 2 (NCBITaxon:2697049)
9
6
74
8,120
5,609
14
8609.50
CCMS System (ccms)
Q Exactive HF-X
+UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:5 - "Carbamylation."
UNIMOD:1 - "Acetylation."
UNIMOD:7 - "Deamidation."
UNIMOD:2016 - "TMTpro 16plex Tandem Mass Tag"
Apr. 28, 2021, 10:52 PM
540,238
158,104
318,931
8,421
21
Inhibition of growth factor signaling prevents SARS-CoV-2 replicationMSV000085494 | PXD018357
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)
+TMT
SARS-CoV-2
COVID-19
Infection
Phospho
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Severe acute respiratory syndrome coronavirus 2 (NCBITaxon:2697049)
2
4
5
3,055
2,253
13
7609.17
CCMS System (ccms)
Orbitrap Fusion Lumos
+UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:28 - "Pyro-glu from Q."
UNIMOD:21 - "Phosphorylation."
UNIMOD:5 - "Carbamylation."
UNIMOD:1 - "Acetylation."
UNIMOD:7 - "Deamidation."
UNIMOD:737 - "Sixplex Tandem Mass Tag."
UNIMOD:4 - "Iodoacetamide derivative."
Apr. 28, 2021, 10:32 PM
77,821
14,758
29,455
3,127
22
GNPS - Proteomic and Metabolomic Characterization of COVID-19 Patient SeraMSV000085507 | PXD019221
CoronaMassKB Hackathon: MassIVE/CCMS MSStats on MS-GF+ reanalysis of MSV000085507 / PXD019221 Proteomic and Metabolomic Characterization of COVID-19 Patient SeraRMSV000000331.2
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
+COVID-19
Proteomics
Metabolomics
Severity
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Severe acute respiratory syndrome coronavirus 2 (NCBITaxon:2697049)
5
5
26
605
305
12
757.25
CCMS System (ccms)
Q Exactive HF
+UNIMOD:4 - "Iodoacetamide derivative."
UNIMOD:2016 - "TMTpro 16plex Tandem Mass Tag"
UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:1 - "Acetylation."
UNIMOD:28 - "Pyro-glu from Q."
Jul. 2, 2020, 2:44 PM
261,984
7,712
15,650
640
23
GNPS - Proteomic and Metabolomic Characterization of COVID-19 Patient SeraMSV000085507 | PXD019221
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.
+COVID-19
Proteomics
Metabolomics
Severity
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Severe acute respiratory syndrome coronavirus 2 (NCBITaxon:2697049)
0
0
0
134
134
8
43841.73
Ting Huang (huang704)
Q Exactive HF
+UNIMOD:4 - "Iodoacetamide derivative."
UNIMOD:2016 - "TMTpro 16plex Tandem Mass Tag"
UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:1 - "Acetylation."
Jun. 17, 2020, 12:26 PM
0
0
0
0
24
GNPS - Proteomic and Metabolomic Characterization of COVID-19 Patient SeraMSV000085507 | PXD019221
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).
+COVID-19
Proteomics
Metabolomics
Severity
MassIVE.quant reviewed - Platinum
CoronaMassKB
ProteoCarta
+Homo sapiens (NCBITaxon:9606)
Severe acute respiratory syndrome coronavirus 2 (NCBITaxon:2697049)
U-937 cells were counted as described above, digested as described above, and serially diluted into 2000, 10, 20, 30, 40, 50, and 60-cell equivalents which were each labeled with TMT11plex tags in two randomized designs with three replicates for each design, for a total of six replicates. These samples were diluted 10x so material corresponding to 200, 1, 2, 3, 4, 5, and 6-cell equivalents was injected and analyzed by LC-MS/MS. For statistical analysis, data preprocessing, protein summarization and statistical testing using MSstatsTMT v1.6.3 was performed. None of normalization is performed, because the assumption for global normalization is not suitable for this experiments and no reference channel is available. R script is available in the 'methods' folder.
+SCoPE2 SCoPE-MS single cell RNA macrophage monocyte
MassIVE.quant reviewed - Gold
Homo sapiens (NCBITaxon:9606)
8
43
72
4,041
2,547
14
109.08
Meena Choi (mnchoi)
Q Exactive
+UNIMOD:7 - "Deamidation."
UNIMOD:35 - "Oxidation or Hydroxylation."
UNIMOD:1 - "Acetylation."
Jun. 12, 2020, 4:48 PM
0
0
0
0
26
A Peptidomimetic Antibiotic Interacts with the Periplasmic Domain of LptD from Pseudomonas aeruginosaMSV000084898 | PXD008577
Additional data for original submission-comparison of abundances between PAL6-labeled and unlabeled LptD/E_HisRMSV000000278.5 | RPXD017557.5
The result for differential analysis for the original submission and the related R script is attached. Note: The differential analysis was performed for each peptide. The data in quant_stat has two separate columns, Protein and PeptideSequence. There are 427 peptides from 2 proteins. Summary for differential proteins and quantified proteins is based on Protein column.
+Gram-negative bacteria
pseudomonas
peptidomimetic antibiotic
Lpt complex
photo crosslinking
DIA
LC-MS/MS
Thermo Q-Exactive Plus
molecular mode of action
MassIVE.quant reviewed - Silver
Pseudomonas aeruginosa PAO1 (NCBITaxon:208964)
2
3
1
2
2
7
3.13
Meena Choi (mnchoi)
Q Exactive
MOD:00425 - "A protein modification that effectively replaces one hydrogen atom with a hydroxyl group."
Jun. 12, 2020, 2:42 PM
0
0
0
0
27
TMT10 controlled mixtures - SILAC HeLa UPS1, acquired using MS2-only strategyMSV000084266 | PXD015261
This reanalysis is the statistical analysis by Proteome Discoverer 2.2.0.388 (Thermo Fisher Scientific). The data processing step in Proteome Discoverer is the same as in RMSV000000266.5. The protein report including protein abundance and statistical testing results was exported from Proteome Discoverer. The parameters when outputting the protein report from PD is the default except for Protein FDR Confidence Combined = c(High, Medium, Low) and Master = c(IsMasterProtein, IsMasterProteinCandidate). We filtered out the proteins whose Master column is IsMasterProteinCandidate so that the results have only one representative protein from each protein group. R script for extracting statistical analysis results is available in the methods folder.
MassIVE.quant reviewed - Platinum
Homo sapiens (NCBITaxon:9606)
4
4
30
5,485
39
11
95.44
Ting Huang (huang704)
Orbitrap Fusion
MOD:00397 - "A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group."
Jun. 8, 2020, 8:59 AM
0
0
0
0
28
TMT10 controlled mixtures - SILAC HeLa UPS1, acquired using MS2-only strategyMSV000084266 | PXD015261
The same PSM report from Proteome Discoverer 2.2.0.388 (Thermo Fisher Scientific) in RMSV000000266.5 was used for this reanalysis. For statistical analysis, data normalization without reference channel, median protein summarization, and statistical testing using limma v3.44.1 was performed. description.pdf including details for data processing by Proteome Discoverer and statistical analysis and R script is available in the 'methods' folder.
MassIVE.quant reviewed - Platinum
Homo sapiens (NCBITaxon:9606)
4
4
30
5,519
305
11
874.59
Ting Huang (huang704)
Orbitrap Fusion
MOD:00397 - "A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group."
Jun. 8, 2020, 8:55 AM
0
0
0
0
29
TMT10 controlled mixtures - SILAC HeLa UPS1, acquired using MS2-only strategyMSV000084266 | PXD015261
The same PSM report from Proteome Discoverer 2.2.0.388 (Thermo Fisher Scientific) in RMSV000000266.5 was used for this reanalysis. For statistical analysis, data preprocessing, log(sum) protein summarization, IRS normalization, and statistical testing using edgeR v3.30.3. was performed. description.pdf including details for data processing by Proteome Discoverer and statistical analysis and R script are available in the 'methods' folder.
MassIVE.quant reviewed - Platinum
Homo sapiens (NCBITaxon:9606)
4
4
30
2,340
29
11
852.39
Ting Huang (huang704)
Orbitrap Fusion
MOD:00397 - "A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group."
Jun. 8, 2020, 8:52 AM
0
0
0
0
30
TMT10 controlled mixtures - SILAC HeLa UPS1, acquired using SPS-MS3MSV000084264 | PXD015258
Raw data were processed using Proteome Discoverer 2.2.0.388 (Thermo Fisher Scientific) and Mascot Server 2.6.1 (Matrix Science, London). Processing workflows were designed to perform a two-pass search on the MS2 data. First, the data were searched against the UniProt/SwissProt human protein database (07.2018 release, 20398 entries) using trypsin/P as an enzyme, a maximum of two missed cleavage sites, and 10 ppm, as the precursor ion mass tolerance. 0.5 and 0.1 Da were specified as the fragment ion mass tolerances for MS3 and MS2, respectively. Carbamidomethylated cysteines (+57.02146 Da), TMT10 and SILAC K8 labeled lysines (+237.177131 Da), SILAC R10 arginines (+10.008269 Da), and TMT10 labeled peptide N-termini (+229.162932 Da) were set as static, while oxidized methionines (+15.99492 Da) were set as dynamic modifications. Second, the data were searched against the human protein database for which the endogenous sequence were replaced with UPS sequences (protein entries marked with ups, 20395 entries), using carbamidomethylated cysteines, TMT10 labeled lysines and peptide Ntermini as static, and oxidized methionines as dynamic modifications. The peptide-to-spectrum matches (PSMs) false discovery rates (FDRs) were controlled using Percolator and setting a max. delta Cn of 0.05 and a q-value threshold of 0.01. Reporter ion quantitation was performed using the MS3 data order (SPS-MS3 method), 3 mmu peak integration and most confident centroid tolerances. Reporter ion intensities were adjusted to correct for the isotopic impurities of the different TMT reagents (manufacturer specifications). Reporter ions intensities were used to express abundances. PSMs from all ranks were considered, peptide FDRs were controlled by setting a q-value threshold of 0.01 and allowing the software to automatically select PSM q-value or ion score for the grouping (PSM FDR was 0.89%, peptide group FDR was 1.21%). High confidence peptides with a minimal length of 6 residues were further grouped into proteins and protein FDR was set to fulfill a q-value threshold of 0.01. At this level, protein FDR was 1.09%. For protein grouping, strict parsimony principle was applied. The report for PSM level from Proteome Discoverer was used for downstream statistical analysis. 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. description.pdf including details for data processing by Proteome Discoverer and statistical analysis and R script are available in the methods folder.
MassIVE.quant reviewed - Platinum
Homo sapiens (NCBITaxon:9606)
4
4
30
4,812
26
26
271.61
Ting Huang (huang704)
Orbitrap Fusion
MOD:00397 - "A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group."