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ProteomicsSWATH-MS in quality control of biologicals: Towards confident label-free and non-targeted quantification with single injection? - An illustration with plasma residuals profiling in human immunoglobulin.
By performing data-independent acquisition (DIA), SWATH-MS is expected to provide comprehensive and repeatable spectral data that can be perpetually interrogated by reference spectral libraries. In the context of biological sample quality control, a benchmark spectral library could index all the pos...
ORGANISM(S): Homo sapiens (Human) 
2022-10-04 | PXD007656 | Pride
Single injection Immunoglobulin Tripletof5600 Biologicals Swath ms 
ProteomicsPhospho-iTRAQ - Phospho-iTRAQ: Assessing Isobaric Labels for the Large-Scale Study Of Phosphopeptide Stoichiometry
One of the most extensively studied protein modifications is phosphorylation, a reversible posttranslational modification (PTM) with a central role in a broad range of cellular processes such as cell metabolism, homeostasis, transcription and apoptosis. Due to their transient character, phosphorylat...
ORGANISM(S): Homo sapiens (Human) 
2015-01-30 | PXD001574 | Pride
Itraq Phosphoproteomics Pitraq 
ProteomicsHistone datasets for evaluation of histone extraction protocols
Extracting histones from cells is a routine operation for studies that aim to characterize histones and their post-translational modifications (hPTMs). However, label-free quantitative mass spectrometry (MS) approaches, both data-dependent (DDA) and data-independent (DIA), require streamlined protoc...
ORGANISM(S): Homo sapiens (Human) 
2016-10-11 | PXD002885 | Pride
Extraction protocols Label-free ms Histone Targeted and untargeted analysis 
ProteomicsCandidate Treponema pallidum biomarkers uncovered in human urine samples from MSM individuals with syphilis using a multi-platform mass spectrometry approach
Background A molecular diagnostic test that could directly evaluate Treponema pallidum subspecies pallidum antigens in urine would greatly facilitate the prompt diagnosis of syphilis. Methods A multi-platform high resolution shotgun proteomics approach was used to investigate the presence of T. pal...
ORGANISM(S): Homo sapiens (Human) 
2018-10-18 | PXD009707 | Pride
Mass spectrometry  syphilis  treponema pallidum  biomarker discovery  antigen test  urine  data independent acquisition  proteomics 
ProteomicsPlasma functionalization of PCL nanofibers changes protein interactions with cells resulting in increased cell viability
The surface properties of electrospun scaffolds can greatly influence protein adsorption and thus strongly dictate cell-material interactions. In this study, we aim to investigate possible correlations between the surface properties of argon, nitrogen and ammonia/helium plasma-functionalized polycap...
ORGANISM(S): Homo sapiens (Human) 
2018-08-29 | PXD010910 | Pride
Human Synaptg2si Functionalized plasma Hff Nanofibres 
TranscriptomicsExpression profiling of laser-microdissected tissue from Tg2576 plaque-depositing mouse model of Alzheimer's disease
Amyloid-M-CM-^_ (AM-CM-^_) plaques are pathological hallmarks of Alzheimer disease. However, the precise neuropathological changes that occur in brain in response to amyloid deposition are largely unknown. To study the molecular mechanism(s) responsible for AM-CM-^_-mediated neuropathology, we perfo...
ORGANISM(S): Mus musculus 
2014-11-04 | E-GEOD-15056 | biostudies-arrayexpress
TranscriptomicsExpression profiling of laser-microdissected tissue from APPPS1 plaque-depositing mouse model of Alzheimer's disease
Amyloid-M-CM-^_ (AM-CM-^_) plaques are pathological hallmarks of Alzheimer disease. However, the precise neuropathological changes that occur in brain in response to amyloid deposition are largely unknown. To study the molecular mechanism(s) responsible for AM-CM-^_-mediated neuropathology, we perfo...
ORGANISM(S): Mus musculus 
2014-11-04 | E-GEOD-15058 | biostudies-arrayexpress
ProteomicsComparison of fractionation proteomics for local SWATH library building
For data-independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data-dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. Th...
ORGANISM(S): Homo sapiens (Human) 
2017-07-04 | PXD006190 | Pride
Library building Comparative study Swath-ms Fractionation proteomics Hesc 
ProteomicsOptimization of SILAC in human embryonic stem cells
We present a fully defined culture system (adapted Essential8 (E8) medium in combination with vitronectin) for human embryonic stem cells (hESC) that can be used for Stable Isotopic Labeling of Amino aCids (SILAC) purposes. Although a complete incorporation of the labels was observed after 4 days in...
ORGANISM(S): Homo sapiens (Human) 
2016-07-15 | PXD002859 | Pride
Culture Silac Hesc 
TranscriptomicsPlate-based long-read single cell gene- and isoform transcriptome profiling using scLIS-seq
Single cell RNA-profiling in tandem with short-read sequencing (SR-scRNA-seq) has revolutionized the field of transcriptomics, permitting a highly granular view on cellular blood and tissue composition and the construction of human cell atlases. However, discrimination between various transcript iso...
ORGANISM(S): Homo sapiens 
2025-12-31 | E-MTAB-15047 | biostudies-arrayexpress
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