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ProteomicsA method for independent estimation of false localisation rate for phosphoproteomics
Phosphoproteomics methods are commonly employed in labs to identify and quantify the sites of phosphorylation on proteins. In recent years, various software tools have been developed, incorporating scores or statistics related to whether a given phosphosite has been correctly identified, or to estim...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) Homo sapiens (Human) 
2022-06-09 | PXD028840 | Pride
False localisation Phosphorylation 
UnknownMembrane topography and the overestimation of protein clustering in single molecule localisation microscopy - identification and correction.
Not available
S-EPMC11217499 | biostudies-literature
ProteomicsLocalisation of outer membrane proteins in Treponema denticola by quantitative proteome analyses of outer membrane vesicles and cellular fractions
The identification and localisation of outer membrane proteins (Omps) and lipoproteins in pathogenic treponemes such as T. denticola (periodontitis) and T. pallidum (syphilis) has been challenging largely due to the structural uniqueness of their outer membranes (OM), the high abundance of inner mem...
ORGANISM(S): Treponema denticola ATCC 35405 
2019-02-20 | PXD011495 | Pride
Treponema denticola Localization Outer membrane vesicles Bacterial lipoproteins Maxquant Outer membrane proteins Orbitrap 
UnknownComparison of observer based methods for source localisation in complex networks.
Not available
S-EPMC8948209 | biostudies-literature
TranscriptomicsThe impact of P53 loss on transcriptome changes following loss of Apc in the intestine
BACKGROUND: p53 is an important tumor suppressor with a known role in the later stages of colorectal cancer, but its relevance to the early stages of neoplastic initiation remains somewhat unclear. Although p53-dependent regulation of Wnt signalling activity is known to occur, the importance of thes...
ORGANISM(S): Mus musculus 
2015-06-25 | E-GEOD-70262 | biostudies-arrayexpress
ProteomicsPhosphorylation in the Plasmodium falciparum proteome: A meta-analysis of publicly available data sets
Malaria is a deadly disease caused by Apicomplexan parasites of the Plasmodium genus. Several species of the Plasmodium genus are known to be infectious to human, of which P. falciparum is the deadliest. Post-translational modifications (PTMs) of proteins coordinate cell signalling and hence, regula...
ORGANISM(S): Plasmodium falciparum 
2023-11-22 | PXD046874 | Pride
Phosphoproteomics Ptmexchange Flr Public data Reanalysis 
ProteomicsSimultaneous characterisation of RNA and protein subcellular dynamics
Existing methods to analyse RNA localisation are constrained to specific RNAs or subcellular niches, precluding the cell-wide mapping of RNA. We present Localisation of RNA (LoRNA), which maps, at once, RNAs to membranous (nucleus, ER and mitochondria) and membraneless compartments (cytosol, nucleol...
ORGANISM(S): Homo sapiens (Human) 
2022-01-25 | PXD030456 | Pride
Dynamics Subcellular localisation Tmt Spatial-proteome Lopit 
ProteomicsLocalisation of Organelle Proteins using Data-Independent Acquisition (DIA-LOP)
Subcellular localisation within the proteome fundamentally influences cellular processes, however the development of high-throughput techniques to allow proteome-wide mapping of the cell has proven difficult. Here we present DIA-LOP, an approach capable of high-throughput spatial proteome mapping wi...
ORGANISM(S): Homo sapiens (Human) 
2025-09-29 | PXD063082 | Pride
Human Lc-msms Dia Diapasef Dda 
ProteomicsInvestigating the protein-protein interactions of EccA3 in Mycobacterium smegmatis
Mycobacterium smegmatis encodes three ESX secretion systems, ESX-1, -3 and -4. Previous research has suggested localisation of the ESX-1 secretion system at the growing polar region of M. smegmatis. In a seperate study, we demonstrated unipolar localisation of EccA3 from ESX-3 at the growing polar r...
ORGANISM(S): Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) Bacteria 
2022-06-09 | PXD018978 | Pride
Ap-ms Esx Mycobacterium smegmatis Polar localisation 
ProteomicsThe Expanding Landscape of Human Protein Phosphorylation C4PR_LIV
Investigation of protein phosphorylation in humans has largely focussed on serine (Ser), threonine (Thr) and tyrosine (Tyr), with proven roles for these modifications in all aspects of life. However, mounting evidence suggests that phosphorylation of non-canonical amino acids, including histidine an...
ORGANISM(S): Homo sapiens (Human) 
2020-06-16 | PXD012188 | Pride
Strong anion exchange Phosphoaspartate Non-canonical phosphorylation Phosphoproteomics Mass spectrometry 
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