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TranscriptomicsTranscriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions
Investigation of whole genome gene expression level changes in Thermoplasma acidophilum cultured under aerobic and anaerobic conditions. The analysis are further described in Na Sun, Cuiping Pan, Stephan Nickell, Matthias Mann, Wolfgang Baumeister, and István Nagy, Quantitative proteome and transcri...
ORGANISM(S): Thermoplasma acidophilum DSM 1728 
2011-09-26 | E-GEOD-21956 | biostudies-arrayexpress
ProteomicsMachine Learning Based Classification of Diffuse Large B-cell Lymphoma Patients by their Protein Expression Profiles
Characterization of tumors at the molecular level has improved our knowledge of cancer causation and progression. Proteomic analysis of their signaling pathways promises to enhance our understanding of cancer aberrations at the functional level, but this requires accurate and robust tools. Here, we ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-30 | MSV000080813 | MassIVE
ProteomicsDeep Visual Proteomics defines single-cell identity and heterogeneity
Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here we introduce Deep Visual Proteomics (DVP), which combines artificial-intelligence-driven ima...
ORGANISM(S): Homo sapiens (Human) 
2022-04-27 | PXD023904 | Pride
Microscopy Digital pathology Proteomics Laser microdissection 
ProteomicsProteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links part 2 of 2: AP-MS DATA (QUBIC)
DNA interstrand crosslinks (ICLs) block replication fork progression by inhibiting DNA strand separation. Repair of ICLs requires sequential incisions, translesion DNA synthesis, and homologous recombination, but the full set of factors involved in these transactions remains unknown. Here we establi...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-03-13 | MSV000079577 | MassIVE
ProteomicsThe Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High Performance Quadrupole and an Ultra-High Field Orbitrap Analyzer
The quadrupole Orbitrap mass spectrometer (Q Exactive) has made a powerful proteomics instrument available in a benchtop format. It significantly boosted analyzable proteins per hour and has now evolved into a proteomics analysis workhorse for many laboratories. Here we describe the Q Exactive Plus ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-04-01 | MSV000080865 | MassIVE
ProteomicsHs_Hela_CellCycle_Phospho
HeLa S3 cells, SILAC labeled
ORGANISM(S): Homo Sapiens (human) 
2010-12-31 | PAe005252 | PeptideAtlas
ProteomicsComparative proteomics of two life cycle stages of stable isotope-labeled Trypanosoma brucei reveals novel components of the parasite's host adaptation machinery.
Trypanosoma brucei developed a sophisticated life cycle to adapt to different host environments. Although developmental differentiation of T. brucei has been the topic of intensive research for decades, the mechanisms responsible for adaptation to different host environments are not well understood....
ORGANISM(S): Trypanosoma brucei 
2014-01-28 | PXD000711 | Pride
Trypanosomes 
ProteomicsUltra-deep human phosphoproteome reveals different regulatory nature of Tyr and Ser/Thr-based signaling
Regulatory protein phosphorylation controls nearly every normal and pathophysiological signaling system in eukaryotic cells. Despite great advances in mass spectrometry based-proteomics, the total number, localization and site-specific stoichiometry of this post-translational modification (PTM) are ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-28 | MSV000080701 | MassIVE
ProteomicsParallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF)
Data independent acquisition modes isolate and concurrently fragment populations of different precursors by cycling through segments of a predefined precursor m/z range. Although these selection windows collectively cover the entire m/z range, overall only a few percent of all incoming ions in each ...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2020-12-17 | PXD017703 | Pride
Tims Pasef Dia Technical Ion mobility 
ProteomicsDeep proteomic evaluation of primary and cell line motoneuron disease models delineates major differences in neuronal characteristics
The fatal neurodegenerative disorders amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA) are the most common motoneuron disease and genetic cause of infant death, respectively. Various in vitro model systems have been established to investigate motoneuron disease mechanisms - in p...
ORGANISM(S): Mus musculus (Mouse) 
2014-09-09 | PXD000666 | Pride
Neuron Amyotrophic lateral sclerosis Als Neurodegeneration Quantitative proteomics Motoneuron 
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