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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
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
ProteomicsCombining label-free and label-based accurate quantifications with SWATH-MS: comparison with SRM and PRM for the evaluation of bovine muscle type effects
The performances of label-based SWATH-MS, SRM and PRM to accurately quantify ten candidate biomarkers of beef meat tenderness or marbling, in a cohort of 64 bovine muscle tissues expected to cover a wide biological range of these traits, were evaluated. Limits of quantification, dynamic range and qu...
ORGANISM(S): Bos taurus (Bovine) 
2021-06-09 | PXD020638 | Pride
Beef meat quality  data-independent acquisition (dia)  quantitative ms  swath-ms  targeted proteomics 
ProteomicsA comprehensive evaluation of common quantification strategies for LC-MS/MS-based spatial proteomics using nanoPOTS
A deep understanding of the tissue microenvironment can provide significant insight into the function of tissue and organs in health and disease states. Spatially resolved proteomics techniques can aid in studying spatial tissue organization and cellular communication in their native microenvironmen...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-03-22 | MSV000091531 | MassIVE
UnknownProteome-Scale Tissue Mapping Using Mass Spectrometry Based on Label-Free and Multiplexed Workflows.
Not available
S-EPMC11541776 | biostudies-literature
UnknownProteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows.
Not available
S-EPMC10942300 | biostudies-literature
UnknownAccurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ.
Not available
S-EPMC4159666 | biostudies-literature
ProteomicsLabel-free quantitative proteomics in Candida yeast species: technical and biological replicates to asses data reproducibility
Objective Label-free quantitative proteomics has emerged as a powerful strategy to obtain high quality quantitative measures of the proteome with only a very small quantity of total protein extract. Because our research projects were requiring the application of bottom-up shotgun Mass Spectrometry p...
ORGANISM(S): Candida albicans (Yeast) Candida glabrata (Yeast) (Torulopsis glabrata) 
2019-07-08 | PXD014125 | Pride
Mass spectrometry  label-free quantitative proteomics  candida glabrata  candida albicans  alkaline ph 
ProteomicsProteomics Complementation of the Rat Uterotrophic Assay for Estrogenic Endocrine Disruptors: A Roadmap of Advancing High Resolution Mass Spectrometry-based Shotgun Survey to Targeted Biomarker Quantifications Authors: Laszlo Prokai *, Fatima Rahlouni, Khadiza Zaman,Vien Nguyen, and Katalin Prokai-Tatrai
The widely used rat uterotrophic assay to assess known and potential estrogenic compounds only considers uterine weight gain as endpoint measurement. To complement this method with an advanced technology that reveals molecular targets, we analyzed changes in protein expression using label-free quant...
ORGANISM(S): Rattus norvegicus (Rat) 
2021-04-23 | PXD023273 | Pride
Strogen-regulated proteins  rat  uterus  liquid chromatography–mass spectrometry quantitative label-free proteomics  targeted pathway analysis  protein networks  endocrine disruption 
ProteomicsA mitochondrion-free eukaryote contains proteins preadapted for import into an exogenous mitochondrion-related organelle
The endobiotic flagellate Monocercomonoides exilis is the only eukaryote known to lose any form of mitochondria and all its associated proteins in its evolutionary past. This final stage of the mitochondrial evolutionary pathway may serve as a model to explain events at their very beginning such as ...
ORGANISM(S): Trichomonas vaginalis 
2023-03-11 | PXD035701 | Pride
Hydrogenosome Protein import Evolution of protein targeting : mitochondrion-free eukaryote 
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