Sort   by:  
 Page size 
ProteomicsConsiderations for peptide and protein error rate control in large-scale targeted DIA analyses
Liquid chromatography coupled to tandem mass spectrometry has become the main method for high-throughput identification and quantification of peptides and the inferred proteins. Discovery proteomics commonly employs data-dependent acquisition in combination with spectrum-centric analysis. The accumu...
ORGANISM(S): Homo sapiens (Human) 
2017-08-03 | PXD004884 | Pride
Proteomics Error rate control Swath-ms Dia 
ProteomicsFrom coarse to fine: The absolute Escherichia coli proteome under diverse growth conditions
Accurate measurements of cellular protein concentrations are invaluable to quantitative studies of gene expression and physiology in living cells. Here, we developed a versatile mass spectrometric workflow based on data-independent acquisition proteomics (DIA/SWATH) together with a novel protein inf...
ORGANISM(S): Escherichia coli 
2021-03-11 | PXD014948 | Pride
Protein sectors Swath Absolute protein quantification Correlation to ribosome profiling Spectral library Dia Peptide query parameters Protein inference 
ProteomicsDevelopment of a Trypanosoma cruzi Strain Typing Assay using MS2 peptide spectral libraries (Tc-STAMS2)
Chagas disease is one of the most important neglected diseases with an estimated number of 12 million infected individuals, the majority living in Central and South America. The Trypanosoma cruzi (T.cruzi) protozoan parasite is the etiological agent of Chagas disease. T.cruzi is highly genetically d...
ORGANISM(S): Trypanosoma cruzi 
2018-03-19 | PXD008088 | Pride
Trypanosoma cruzi  discrete typing units (dtus)  mass spectrometry  spectral matching  strain typing methods 
ProteomicsDynamic profiling of the protein life cycle in response to pathogens (protein)
Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expressio...
ORGANISM(S): Mus musculus 
2015-03-06 | E-GEOD-59792 | biostudies-arrayexpress
ProteomicsProteogenomics of Tistlia consotensis
Tistlia consotensis is a halotolerant Rhodospirillaceae that was isolated from a saline spring located in the Colombian Andes with a salt concentration close to seawater (4.5%w/vol). We cultivated this microorganism in three NaCl concentrations, i.e. optimal (0.5%), without (0.0%) and high (4.0%) sa...
ORGANISM(S): Bacteria 
2012-12-18 | PXD000094 | Pride
Draft genome Proteogenomics Rhodospirillaceae Halotolerance Alphaproteobacteria 
TranscriptomicsGlobal expression profiling of low temperature induced genes in chilling tolerant japonica rice
Three week old seedlings of rice cultivar Jumli Marshi (spp. Japonica) was exposed to cold (+4C) temperatures for varying time periods. Tissue samples were collected in replicates. Microarray data analysis was then performed on the extracted totalRNA from the samples.
ORGANISM(S): Oryza sativa japonica 
2013-05-01 | E-MEXP-3718 | biostudies-arrayexpress
UnknownData-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial.
Not available
S-EPMC6088389 | biostudies-literature
ProteomicsThe Paulinella chromatophore N-terminome
The cercozoan amoeba Paulinella chromatophora contains photosynthetic organelles - termed chromatophores - that evolved from a cyanobacterium ~100 million years ago, independently from plastids in plants and algae. Despite its more recent origin, at least one third of the chromatophore proteome cons...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2023-04-06 | PXD028527 | Pride
Protein import Chromatophore Paulinella chromatophore 
ProteomicsEvolutionary quantitative proteomics of reproductive interactions in Drosophila
We present data using a novel method to simultaneously identify and quantify transferred male seminal proteins and the female reproductive proteome using multiplexed Tandem-Mass-Tag (TMT) isobaric labelling of the lower female reproductive tracts dissected from virgin- or recently mated- females of ...
ORGANISM(S): Drosophila novamexicana Drosophila americana Drosophila virilis 
2023-10-24 | PXD031638 | Pride
Drosophila novamexicana Drosophila americana Tmt Sperm Seminal fluid proteins Female reproductive tract Reproductive isolation Postmating prezygotic isolation Drosophila virilis 
ProteomicsVHL Cancer - Proteomic analysis of signaling network regulation in renal cell carcinomas with differential hypoxia-inducible factor-2α expression
The loss of von Hippel-Lindau (VHL) protein function leads to highly vascular renal tumors characterized by an aggressive course of disease and refractoriness to chemotherapy and radiotherapy. Loss of VHL in renal tumors also differs from tumors of other organs in that the oncogenic cascade is medi...
ORGANISM(S): Homo sapiens (Human) 
2013-08-12 | PXD000335 | Pride
Human Vhl Cancer Hif-2a Lc-ms/ms 
Sort   by:  
 Page size