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ProteomicsMaxLFQ label-free quantification algorithm benchmark datasets
We developed a set of algorithms for label-free quantification, termed MaxLFQ, embedded into MaxQuant. This contains two datasets to benchmark MaxLFQ: The proteome benchmark dataset consists of of HeLa and E. coli lysates mixed at defined ratios. The dynamic range benchmark dataset consists of UPS1...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) 
2017-12-19 | MSV000081831 | MassIVE
ProteomicsLFQbench enables a multi-centered benchmark study demonstrating robust proteomic label-free quantification
The consistent and accurate quantification of proteins is a challenging task for mass spectrometry (MS)-based proteomics. SWATH-MS uses data-independent acquisition (DIA) for label-free quantification. Here we evaluated five software tools for processing SWATH-MS data: OpenSWATH, SWATH2.0, Skyline, ...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) Saccharomyces Cerevisiae (ncbitaxon:4932) 
2017-04-27 | MSV000081024 | MassIVE
ProteomicsCombining label-free and label-based accurate quantifications with SWATH-MS: comparison with SRM and PRM for the evaluation of bovine muscle type effects.
Mass spectrometry has proven to be a valuable tool for the accurate quantification of proteins. In this study, we have evaluated the performances of three targeted approaches, namely Selected Reaction Monitoring (SRM), Parallel Reaction Monitoring (PRM) and Sequential Windowed Acquisition of Theoret...
ORGANISM(S): Bos Taurus 
2021-06-08 | PXD020680 | panorama
ProteomicsComparison of Lung Cancer Proteome Profiles 1: Label Free Quantification
The goal of this project is to compare label free quantification, chemical labeling with tandem mass tags, and data independent acquisition discovery proteomics approaches using lung squamous cell carcinomas and adjacent lung tissues.
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-27 | MSV000080685 | MassIVE
ProteomicsLabel-Free Absolute Protein Quantification with Data-Independent Acquisition
Label-free absolute quantitative proteomics is commonly used for absolute quantification of the proteome or specific proteins of interest in various biological samples. Current label-free absolute protein quantification (APQ) methods determine MS1 intensities, MS2 spectral counts or intensities to a...
ORGANISM(S): Homo sapiens (Human) 
2019-03-20 | PXD010912 | Pride
Human Dia S9 Absolute protein quantification Microsome Liver Dda 
ProteomicsLabel-free quantification of busulfan-treated testis
The busulfan-treated mouse model showed abnormal testis morphology and reduced sperm number and testis weight. Testicular and sperm damage was most severe at 30 days after busulfan treatment. The protein level of MGAT1 was increased in busulfan-treated mouse testis. The busulfan-treated mouse testes...
ORGANISM(S): Mus musculus (Mouse) 
2025-05-06 | PXD035492 | Pride
Testis Busulfan Label-free quantification Spermatogenesis 
ProteomicsSurfactant-assisted one-pot sample preparation for label-free single-cell proteomics
Large numbers of cells are generally required for quantitative global proteome profiling due to the significant surface adsorption losses associated with sample processing. Such bulk measurement obscures important cell-to-cell variability (cell heterogeneity) and makes proteomic profiling impossible...
ORGANISM(S): Homo Sapiens 
2021-03-11 | PXD022827 | panorama
ProteomicsLFQbench enables a multi-centered benchmark study demonstrating robust proteomic label-free quantification
The consistent and accurate quantification of proteins is a challenging task for mass spectrometry (MS)-based proteomics. SWATH-MS uses data-independent acquisition (DIA) for label-free quantification. Here we evaluated five software tools for processing SWATH-MS data: OpenSWATH, SWATH2.0, Skyline, ...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2016-09-27 | PXD002952 | Pride
Lfqbench Lfq Swath-ms Benchmark 
ProteomicsLabel-free Quantification of Host-Cell Protein Impurity in a Recombinant Hemoglobin Reference Material
Quantitative analysis depends on pure-substance primary calibrators with known mass fractions of impurity. The datasets included were generated using mass spectrometry for the evaluation of label-free quantification (LFQ) as a method for determining the mass fraction of host-cell proteins (HCPs) in...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2023-05-09 | PXD041736 | Pride
Protein reference materials Dda-pasef Label-free quantification Host-cell proteins 
ProteomicsLabel-free quantification in ion-mobility enhanced data-independent acquisition proteomics
Data-dependent acquisition (DDA) methods are a well-established tool for proteome analysis and have greatly expedited the field of shotgun proteomics. However, their serial and stochastic nature restricts their reproducibility and limits the detectable dynamic range to the peptides that ionize best....
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (strain Lalvin EC1118 / Prise de mousse) (Baker's yeast) Escherichia coli 
2016-03-29 | PXD002393 | Pride
Proteomics Mass spectrometry Label-free quantification Ion mobility separation Data-independent acquisition 
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