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MetabolomicsDIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics
The extraction of meaningful biological knowledge from high-throughput mass spectrometry data relies on limiting false discoveries to a manageable amount. For targeted approaches in metabolomics a main challenge is the detection of false positive metabolic features in the low signal-to-noise ranges ...
2022-09-05 | MTBLS1108 | MetaboLights
ProteomicsSWATH-MS Analysis of Striatal Synaptic Mitochondria from Pink1 KO rats
This study investigates the proteomic alterations in striatal synaptic mitochondria isolated from 3-month-old wild-type and Pink1 KO rats using the SWATH-MS strategy. This dataset consists of 32 raw MS files, comprising 8 DIA (SWATH) and 24 DDA runs on a TripleTOF 5600 (SCIEX). Our findings revealed...
ORGANISM(S): Rattus norvegicus (Rat) 
2016-09-28 | PXD004558 | Pride
Swath-ms Mitochondria Parkinson's disease 
ProteomicsSWATH-MS identification of CXCL7, LBP, TGFβ1 and PDGFRβ as novel biomarkers in human systemic mastocytosis.
We carried out a novel clinical biomarker investigation of the blood of systemic mastocytosis patients versus healthy controls; utilizing a new and emerging technology platform Sequential Window Acquisition of all Theoretical fragment-ion spectra mass spectrometry (SWATH-MS). This is the first use ...
ORGANISM(S): Homo sapiens (Human) 
2022-05-20 | PXD030947 | Pride
Mastocytosis Swath-ms Biomarkers 
ProteomicsAssessing Technical and Biological Variation in SWATH-MS -based Proteomics: A case study in Chronic Lymphocytic Leukaemia
Chronic lymphocytic leukaemia (CLL) is renowned for its variable clinical course and response to therapy, suggesting a role for precision medicine. However, the molecular basis of CLL variability remains incompletely understood. Recent developments in data independent acquisition (DIA) -MS technolog...
ORGANISM(S): Homo sapiens (Human) 
2021-02-08 | PXD011330 | Pride
Cll Swath Leukaemia 
ProteomicsDIA/SWATH-MS analysis of Halobacterium salinarum NRC-1 collected at four time points of batch culture growth
Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requires a priori generated spectral assay libraries. Such assay libraries allow to e...
ORGANISM(S): Halobacterium salinarum 
2023-09-21 | PXD042774 | Pride
Dia Data-independent acquisition Swath Halobacterium salinarum nrc-1 Spectral assay library Dda Data-dependent acquisition 
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 
ProteomicsSWATH-MS Analysis of Gfi1-mutant bone marrow neutrophils
This study investigates the proteomic alterations in bone marrow neutrophils isolated from 5-8 week old Gfi1+/-, Gfi1K403R/-, Gfi1R412X/-, and Gfi1R412X/R412X mice using the SWATH-MS technique. This dataset consists of 26 raw MS files, comprising 13 DDA (for spectral library generation)and 13 DIA (f...
ORGANISM(S): Mus musculus (Mouse) 
2020-04-07 | PXD010943 | Pride
Scn Gfi1 Swath Neutrophil 
ProteomicsGlobal proteome rearrangement screen in interphasic and mitotic HeLa CCL2 cell line by SEC-SWATH-MS
It has become increasingly clear that biological functions depend not only on the identity and quantity, but also the correct interplay among the biomolecules that constitute the cell. Importantly, proteins as the key effectors in the cell dynamically organize into complexes. This study describes a ...
ORGANISM(S): Homo sapiens (Human) 
2019-05-10 | PXD010288 | Pride
Human Protein-protein complexes Hela Cell cycle Swath-ms Sec Mitosis 
ProteomicsE.coli - Whole organism, DIA, SWATHMS (Midhaetal,scidata2020)
abundance based on DIA, SWATHMS, Interaction consistency score: 8.2, Coverage: 49
ORGANISM(S): 511145 
2020-00-00 | 171934967 | PAXDB
ProteomicsYeast Nat Nt-acetylation SWATH MS
Yeast strains (wild type, Naa10 KO and Naa20 KO, resp: wt, natA-delta and natB-delta) were profiled for full proteome analysis by SWATH MS
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-12-15 | PXD015217 | Pride
Nt-acetylation Dia Nata Natb Swath ms Yeast 
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