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ProteomicsUntargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire
Untargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-04-01 | MSV000080875 | MassIVE
Proteomics,MultiomicsDIA-Umpire: comprehensive computational framework for data independent acquisition proteomics
This dataset consists of 44 raw MS files, comprising 27 DIA (SWATH) and 15 DDA runs on a TripleTOF 5600 and of two raw mass spectrometry files acquired on a Q Exactive. The composition of the dataset is described in the manuscript by Tsou et al., titled: "DIA-Umpire: comprehensive computational fra...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) 
2017-04-27 | MSV000081023 | MassIVE
ProteomicsRAD51AP1 regulates ALT-HDR through chromatin-directed homeostasis of TERRA
Alternative lengthening of telomeres (ALT) is a homology-directed repair (HDR) mechanism of telomere elongation that controls proliferation in subsets of highly aggressive cancer. Recent studies have revealed that TERRA (telomere repeat-containing RNA) acts to initiate ALT-associated HDR (ALT-HDR). ...
ORGANISM(S): Homo sapiens (Human) 
2024-01-26 | PXD035943 | Pride
Cancer Alt Terra Homology-directed repair Chromatin Transcription Telomere Rad51ap1 
ProteomicsA systematic screening pipeline identifies a new regulator of tyrosinated microtubule dynamics
Tubulin detyrosination is a reversible post-translational modification thought to be important for processes including the generation of cell polarity and cell division. The Y/ΔY cycle does not affect the intrinsic properties of microtubules per se, but rather influences the cohort of microtubule-as...
ORGANISM(S): Homo sapiens (Human) 
2022-08-16 | PXD030448 | Pride
Microtubule Detyrosination Tmt6 Human Tyrosination Lc-ms/ms 
ProteomicsRe-analysis of glycoproteomics data with MSFragger-Glyco
Reanalysis of submissions PXD011533 and PXD009476 using MSFragger-Glyco mode. Processed MSFragger results files (pepXML) and PSM tables (psm.tsv) supporting MSFragger-Glyco manuscript (Fast and Comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Recent advances in methods for enric...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2020-10-06 | PXD021196 | Pride
Glycosylation Glycoproteomics Msfragger Reanalysis O-glycosylation Glycan Glycopeptide N-glycosylation 
ProteomicsDIA-Umpire: comprehensive computational framework for data independent acquisition proteomics
This dataset consists of 44 raw MS files, comprising 27 DIA (SWATH) and 15 DDA runs on a TripleTOF 5600 and of two raw mass spectrometry files acquired on a Q Exactive. The composition of the dataset is described in the manuscript by Tsou et al., titled: "DIA-Umpire: comprehensive computational fra...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2015-01-21 | PXD001587 | Pride
Swath Dia 
ProteomicsUntargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire
Untargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire
ORGANISM(S): Homo sapiens (Human) 
2016-06-16 | PXD003179 | Pride
Human Dia Dia-umpire 
ProteomicsExpanding glycopeptide identification with Match-Between-Glycans (MBG) in FragPipe
Glycosylation is one of the most important, but also most complex, post-translational modifications of proteins. Mass spectrometry-based glycoproteomics analysis offers a powerful approach to explore the fundamental roles of glycosylation, but achieving sufficient fragmentation for glycopeptide assi...
ORGANISM(S): Candida albicans (Yeast) Mus musculus (Mouse) Homo sapiens (Human) 
2026-09-01 | PXD074575 | Pride
Human plasma  glycoproteomics  n-glycopeptides  pasef  timstof  msfragger-glyco  fragpipe  ion mobility 
ProteomicsMicroplastics and algal toxins in mussels: A dual threat to marine health and seafood safety
The molecular responses of marine mussels to contamination with emergent contaminants in marine ecosystems - the biotoxin Okadaic Acidc and Microplastics - was investigated in experiments with live mussels of the species Perna perna. In total 24 independent biological samples, from 4 experimental co...
ORGANISM(S): Perna perna 
2026-07-16 | PXD071829 | Pride
Shotgun proteomics  perna perna  environmental contamination  ecotoxicology 
ProteomicsIntegrative proteo-genomic profiling uncovers key biomarkers of lapatinib resistance in HER2-positive breast cancer
To understand the transcriptomic, genomic and proteomics changes between HER2 overexpressingcells and those that have become resistant to lapatinib
ORGANISM(S): Homo sapiens (Human) 
2025-11-17 | PXD056848 | Pride
3d Chromatin Proteomics Epigenetics Resistance Her2 Lc-ms/ms 
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