MassIVE.quant Reanalyses

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Submitted MassIVE Reanalyses
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# FilesTotal Size (MB)Uploaded ByInstrumentPTMsUpload DatePSMsPeptidesVariantsProteins
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1
  • Spike-in benchmark study : Ubiquitination, Label-free experiments
    MSV000088971
MSstatsPTM Analysis of Spike-in benchmark study with comparison to limma and ANOVA
RMSV000000669.1
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.
  • +quantitative mass spectrometry
  • +Homo sapiens (NCBITaxon:9606)
00016,8667,86117178.30Devon Kohler (devonjkohler)
  • Orbitrap Fusion Lumos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Aug. 28, 2022, 10:07 AM0000
2
MassIVE/CCMS MSStats on Maestro /MaxQuant reanalysis of MSV000082204 / PXD005940 Global Proteome Analysis of the NCI-60 Cell Line Panel
RMSV000000631.1 | RPXD033211.1
MassIVE/CCMS MSStats on Maestro /MaxQuant reanalysis of MSV000082204 / PXD005940 Global Proteome Analysis of the NCI-60 Cell Line Panel
  • Proteomics
  • Homo sapiens (NCBITaxon:9606)
1914,1740119941.25CCMS System (ccms)
  • LTQ Orbitrap Elite
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 13, 2022, 1:15 PM1,447,93690,341165,8377,430
3
MassIVE/CCMS MSStats on Maestro reanalysis of MSV000086387 / PXD016999 A Quantitative Proteome Map of the Human Body
RMSV000000635.1 | RPXD033216.1
MassIVE/CCMS MSStats on Maestro reanalysis of MSV000086387 / PXD016999 A Quantitative Proteome Map of the Human Body
  • Proteomics
  • Homo sapiens (NCBITaxon:9606)
335629,1548,91311511297.20CCMS System (ccms)
  • Orbitrap Fusion
  • +UNIMOD:4 - "Iodoacetamide derivative."
Apr. 13, 2022, 12:57 PM5,480,723208,696489,49013,465
4
  • Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors
    MSV000085343 | 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 tumors
RMSV000000630.1 | 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)
32714,60486111231.44CCMS System (ccms)
  • Orbitrap Fusion
  • +UNIMOD:4 - "Iodoacetamide derivative."
Apr. 13, 2022, 12:14 PM249,27638,58657,8724,675
5
  • Shigella Ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infection
    MSV000088966
MSstatsPTM Analysis of Shigella Ubiquitin ligase IpaH7.8 Experiment
RMSV000000356.1
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
  • Homo sapiens (NCBITaxon:9606)
00016,9696,58010207.29Devon Kohler (devonjkohler)
  • Orbitrap Fusion Lumos
  • +MOD:01060 - "A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine."
Mar. 7, 2022, 7:57 AM0000
6
May Institute 2021- massive.quant hands-on
RMSV000000345.1 | RPXD026005.1
this is the result using MSstats during May Institute 2021 week2 hands-on session.
  • +yeast
  • Saccharomyces cerevisiae (NCBITaxon:4932)
6312,0698109198.91Meena Choi (mnchoi)
  • +TripleTOF 5600
  • +00935
May. 13, 2021, 11:08 AM0000
7
  • +
    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
  • +omics
  • +Homo sapiens (NCBITaxon:9606)
216942,9122,3421517581.92CCMS System (ccms)
  • +LTQ Orbitrap
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 30, 2021, 10:59 AM3,496,46633,110108,6223,710
8
  • 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
  • +SARS-CoV-2
  • +Homo sapiens (NCBITaxon:9606)
3195129,6794,410428852.38CCMS System (ccms)
  • Exactive Plus
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 7:19 PM766,39832,52987,5112,705
9
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
  • +TMT
  • +Homo sapiens (NCBITaxon:9606)
2156,6764,01912411.13CCMS System (ccms)
  • Orbitrap Fusion Lumos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 7:00 PM145,43877,953104,9386,815
10
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
  • +TMT
  • +Homo sapiens (NCBITaxon:9606)
2153,5052,69512152.64CCMS System (ccms)
  • Orbitrap Fusion Lumos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 6:53 PM42,15912,21721,6643,611
11
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
  • +omics
  • +Homo sapiens (NCBITaxon:9606)
1014812,8271211311436.10CCMS System (ccms)
  • LTQ Orbitrap Velos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 6:46 PM1,003,54630,81088,6213,166
12
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
  • +Urine proteomics
  • +Homo sapiens (NCBITaxon:9606)
44032,232902139415.13CCMS System (ccms)
  • Orbitrap Fusion Lumos
  • +UNIMOD:4 - "Iodoacetamide derivative."
Apr. 29, 2021, 6:35 PM1,183,41941,198101,8122,543
13
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
  • +Homo sapiens (NCBITaxon:9606)
2456,4573,468137760.01CCMS System (ccms)
  • Orbitrap Fusion Lumos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 6:16 PM165,20566,353100,7816,575
14
  • +
    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
  • +omics
  • +Homo sapiens (NCBITaxon:9606)
1015012,8591,4341412727.38CCMS System (ccms)
  • LTQ Orbitrap Velos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 6:06 PM1,870,96029,92085,9683,174
15
  • +
    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
  • +omics
  • +Homo sapiens (NCBITaxon:9606)
1015013,4752911416417.94CCMS System (ccms)
  • LTQ Orbitrap Velos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 5:20 PM3,697,34333,76065,3223,731
16
  • 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
  • +omics
  • +Homo sapiens (NCBITaxon:9606)
363012,5103321410760.24CCMS System (ccms)
  • LTQ Orbitrap
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 5:02 PM648,16622,07748,2962,713
17
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
  • +omics
  • +Homo sapiens (NCBITaxon:9606)
126412,03683159355.84CCMS System (ccms)
  • LTQ Orbitrap
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 3:52 PM432,77018,21441,6962,209
18
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
  • +coronavirus
  • +Betacoronavirus sp. (NCBITaxon:1928434)
22101,6221,008149197.30CCMS System (ccms)
  • Q Exactive HF
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 29, 2021, 3:35 PM930,91914,03623,3191,882
19
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
  • +COVID-19
  • +Homo sapiens (NCBITaxon:9606)
591233712051310219.80CCMS System (ccms)
  • Q Exactive HF
  • +UNIMOD:4 - "Iodoacetamide derivative."
Apr. 28, 2021, 11:33 PM1,339,85420,141135,257335
20
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
  • +COVID19
  • +Homo sapiens (NCBITaxon:9606)
96748,1205,609148609.50CCMS System (ccms)
  • Q Exactive HF-X
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 28, 2021, 10:52 PM540,238158,104318,9318,421
21
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
  • +Homo sapiens (NCBITaxon:9606)
2453,0552,253137609.17CCMS System (ccms)
  • Orbitrap Fusion Lumos
  • +UNIMOD:35 - "Oxidation or Hydroxylation."
Apr. 28, 2021, 10:32 PM77,82114,75829,4553,127
22
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
  • +COVID-19
  • +Homo sapiens (NCBITaxon:9606)
552660530512757.25CCMS System (ccms)
  • Q Exactive HF
  • +UNIMOD:4 - "Iodoacetamide derivative."
Jul. 2, 2020, 2:44 PM261,9847,71215,650640
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.
  • +COVID-19
  • +Homo sapiens (NCBITaxon:9606)
000134134843841.73Ting Huang (huang704)
  • Q Exactive HF
  • +UNIMOD:4 - "Iodoacetamide derivative."
Jun. 17, 2020, 12:26 PM0000
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).
  • +COVID-19
  • +Homo sapiens (NCBITaxon:9606)
567207863391844012.65Ting Huang (huang704)
  • Q Exactive HF
  • +UNIMOD:4 - "Iodoacetamide derivative."
Jun. 17, 2020, 10:21 AM0000
25
MassIVE.quant-ladder experiment-MaxQuant+MSstatsTMT
RMSV000000326.2
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
  • Homo sapiens (NCBITaxon:9606)
843724,0412,54714109.08Meena Choi (mnchoi)
  • Q Exactive
  • +UNIMOD:7 - "Deamidation."
Jun. 12, 2020, 4:48 PM0000
26
  • A Peptidomimetic Antibiotic Interacts with the Periplasmic Domain of LptD from Pseudomonas aeruginosa
    MSV000084898 | PXD008577
Additional data for original submission-comparison of abundances between PAL6-labeled and unlabeled LptD/E_His
RMSV000000278.5 | 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 aeruginosa PAO1 (NCBITaxon:208964)
2312273.13Meena Choi (mnchoi)
  • Q Exactive
  • MOD:00425 - "A protein modification that effectively replaces one hydrogen atom with a hydroxyl group."
Jun. 12, 2020, 2:42 PM0000
27
MassIVE.quant reanalysis from offline PD results
RMSV000000266.8 | RPXD015301.8
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)
44305,485391195.44Ting 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 AM0000
28
MassIVE.quant reanalysis from offline PD+Ratio+Median+Limma results
RMSV000000266.7 | RPXD015301.7
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)
44305,51930511874.59Ting 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 AM0000
29
MassIVE.quant reanalysis from offline PD+Sum+IRS+edgeR results
RMSV000000266.6 | RPXD015301.6
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)
44302,3402911852.39Ting 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 AM0000
30
MassIVE.quant reanalysis from offline PD+MSstatsTMT results
RMSV000000265.13 | RPXD015299.13
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)
44304,8122626271.61Ting 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, 8:15 AM0000

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