MassIVE.quant is an extension of the Mass Spectrometry Interactive Virtual Environment (MassIVE) to provide the opportunity for large-scale deposition of heterogeneous experimental datasets, and facilitate a community-wide conversation about the necessary extent of experiment documentation and the benefits of its use. MassIVE.quant supports various reproducibility scopes, such as the infrastructure to fully automate the workflow, to store, and to browse the intermediate results. In addition, MassIVE.quant provides a collection of consistently documented and analyzed benchmark datasets.

Note: We recommend using either Chrome or Firefox to browse the datasets below. Other web browsers are not supported due to missing or incomplete support for rendering FTP links.

Dataset Title Reanalysis Count Quantification Reanalyses
MSV000079843 IPRG2015 22
MSV000081024 LFQbench enables a multi-centered benchmark study demonstrating robust proteomic label-free quantification 20
MSV000081677 SWATH Analysis of Yeast Proteome over Time in Response to Osmotic Stress 22
MSV000081828 PASS00589 - Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues 15
MSV000081829 PASS00289 - OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data:SWATH-MS Gold Standard (SGS) Dataset, S. pyogenes Dataset 2
MSV000081831 MaxLFQ label-free quantification algorithm benchmark datasets 3
MSV000082569 Extended multiplexing of TMT labeling reveals age and high fat diet specific proteome changes in mouse epididymal adipose tissue 4
  • RMSV000000264.1 - "MassIVE.Quant-Reanalysis-Proteome Discoverer-MSstatsTMT"
  • RMSV000000264.2 - "MassIVE.Quant-Reanalysis-Proteome Discoverer-median+limma"
  • RMSV000000264.3 - "MassIVE.Quant-Reanalysis-Proteome Discoverer-sum(int)+IRS+edgeR"
  • RMSV000000264.4 - "MassIVE.Quant-Reanalysis-Proteome Discoverer-PD"
MSV000084048 Epithelial ovarian cancer biomarker 0
MSV000084181 MSstats splitplot method for protein quantitation in MS datasets 20
MSV000084220 MSstats splitplot method for protein quantitation in MS datasets-SRM controlled mixture 0
MSV000084263 A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments 4
  • RMSV000000267.1 - "MassIVE.Quant-Reanalysis-Proteome Discoverer-MSstatsTMT"
  • RMSV000000267.2 - "MassIVE.Quant-Reanalysis-Proteome Discoverer-median+limma"
  • RMSV000000267.3 - "MassIVE.Quant-Reanalysis-Proteome Discoverer-sum(int)+IRS+edgeR"
  • RMSV000000267.4 - "MassIVE.Quant-Reanalysis-Proteome Discoverer-PD"
MSV000084264 TMT10 controlled mixtures - SILAC HeLa UPS1, acquired using SPS-MS3 4
  • RMSV000000265.1 - "MassIVE.Quant-Reanalysis-Proteome Discoverer-MSstatsTMT"
  • RMSV000000265.2 - "MassIVE.Quant-Reanalysis-Proteome Discoverer-median+limma"
  • RMSV000000265.3 - "MassIVE.Quant-Reanalysis-Proteome Discoverer-sum(int)+IRS+edgeR"
  • RMSV000000265.4 - "MassIVE.Quant-Reanalysis-Proteome Discoverer-PD"
MSV000084266 TMT10 controlled mixtures - SILAC HeLa UPS1, acquired using MS2-only strategy 1

Copyright © 2019. Last modified: 2019-12-03. Version 1.3.2-MassIVE.