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ProteomicsIn vivo and in vitro proteome analysis of HIV-1 infected, human CD4+ T cells
Host directed therapies against HIV-1 are thought to be critical for long term containment of the HIV-1 pandemic but remain elusive. Since HIV-1 infects and manipulates important effectors of both the innate and adaptive immune system, identifying modulations of the host cell systems in humans durin...
ORGANISM(S): Homo sapiens (Human) 
2017-02-28 | PXD005234 | Pride
Cd4 t cell Hiv Swath 
ProteomicsThe Proteome Landscape of Chronic Lymphocytic Leukemia
Many functional consequences of mutations on tumor phenotypes in chronic lymphocytic leukemia (CLL) are only partially known. This is in part due to missing information on the proteome of CLL. We profiled the proteome of 49 diverse CLL samples with data-independent acquisition mass spectrometry (DIA...
ORGANISM(S): Homo sapiens (Human) 
2021-09-27 | PXD022216 | Pride
Leukemia Diapasef Cll 
ProteomicsBuilding high-quality assay libraries for targeted analysis of SWATH MS data
Targeted proteomics by selected/multiple reaction monitoring or, on a larger scale, by SWATH MS relies on spectral reference libraries for peptide identification. Quality and coverage of these libraries are therefore of critical importance. Here we present a detailed protocol that has been successfu...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2015-01-26 | PXD001126 | Pride
Yeast Assay library Swath Spectral library 
ProteomicsEnterococcus faecalis V583, Part 1
Genome-scale models represent the link between an organism's genetic information and experimentally observable biological phenotypes. They facilitate metabolic engineering and the discovery of network properties such as the identification of novel drug targets. Most commonly, metabolite consumption ...
ORGANISM(S): Enterococcus faecalis (Streptococcus faecalis) 
2016-12-06 | PXD001576 | Pride
Swath Ph_shift Efv583 
ProteomicsEnterococcus faecalis V583 - data analysis
Genome-scale models represent the link between an organism's genetic information and experimentally observable biological phenotypes. They facilitate metabolic engineering and the discovery of network properties such as the identification of novel drug targets. Most commonly, metabolite consumption ...
ORGANISM(S): Enterococcus faecalis (Streptococcus faecalis) 
2016-12-06 | PXD002869 | Pride
Swath Ph_shift Efv583 
ProteomicsMulti-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
Quantitative proteomics employing mass spectrometry has become an indispensable tool in basic and applied life science research. Methods based on data-dependent acquisition have proved extremely valuable for qualitative proteome analysis but historically have struggled to achieve reproducible quanti...
ORGANISM(S): Homo sapiens (Human) 
2020-02-19 | PXD004886 | Pride
Reproducibility Proteomics Swath-ms 
TranscriptomicsTranscription profiling of human MCF-7 cells treated with Fulvestrant (ICI 182,780) and vehicle reveals origins and phenotypic variations of antiestrogen resistance in breast cancer
Expression profiles of MCF-7 cells treated with Fulvestrant (ICI 182,780) and vehicle Experiment Overall Design: MCF7 cells were grown in DMEM supplemented with 5% FCS (Hyclone, "Defined" grade). Growth medium was changed immediately before addition of 100 nM of ICI 182,780 or vehicle alone (0.1% et...
ORGANISM(S): Homo sapiens 
2009-09-15 | E-GEOD-14986 | biostudies-arrayexpress
ProteomicsSWATH analysis of 1433B_HUMAN affinity purifications from HEK293 cells after time course treatment with IGF1
Protein complexes and protein interaction networks are essential mediators of most biological functions. Complexes supporting transient functions such as signal transduction processes are frequently subject to dynamic remodeling. Currently, the majority of studies into the composition of protein com...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-08-20 | MSV000082833 | MassIVE
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 
2022-01-12 | PXD017258 | panorama
ProteomicsPASS00724 - Raw DIA files and libraries used in the manuscript "Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-Independent Acquisition Mass Spectrometry"
Data independent acquisition files and corresponding library files used to demonstrate the value of a set of conserved, commonly occurring peptide sequences to align chromatographic retention time between spectral libraries and DIA files.
ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932) Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) 
2018-08-23 | MSV000082842 | MassIVE
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