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ProteomicsEvaluating False Transfer Rates from the Match-Between-Runs algorithm with a two-proteome model
Stochasticity between independent LC-MS/MS runs is a challenging problem in the field of proteomics resulting in significant missing values (i.e., abundance measurements) among observed peptides. To address this issue, several approaches have been developed including computational methods such as Ma...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2019-09-25 | PXD014415 | Pride
False transfer rate Match-between-runs Label-free quantitation Two-proteome mixture 
ProteomicsLibrary-based virtual match-between-runs quantification scheme enabled by GlyPep-Quant dramatically enhances the identification of site-specific glycans and detection of occupancy ratio changes
Glycosylation changes are closely related to various diseases like cancer. However, the quantitative analysis of the site-specific glycans at proteomics scale remains challenging because of the extremely low interpretation rate of glycopeptide spectra. Here, we present a new software tool, GlyPep-Qu...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) Schizosaccharomyces pombe 
2025-07-06 | PXD057799 | Pride
Proteomics  glycosylation  site-specific glycan  quantification  match-between-runs 
UnknownEvaluating False Transfer Rates from the Match-between-Runs Algorithm with a Two-Proteome Model.
Not available
S-EPMC7346880 | biostudies-literature
UnknownIonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs.
Not available
S-EPMC8131922 | biostudies-literature
UnknownLibrary-based virtual match-between-runs quantification in GlyPep-Quant improves site-specific glycan identification.
Not available
S-EPMC12259847 | biostudies-literature
ProteomicsPeak identification and quantification by proteomic mass spectrogram decomposition
Recent advances in liquid chromatography/mass spectrometry (LC/MS) technology have improved the sensitivity, resolution, and speed of proteome analysis, resulting in demand for sophisticated algorithms to interpret complex mass spectrograms. Here, we propose a novel statistical method, proteomic mas...
ORGANISM(S): Homo Sapiens (human) Saccharomyces Cerevisiae (baker's Yeast) 
2021-03-06 | PXD015189 | JPOST Repository
ProteomicsIsobaric matching between runs and novel PSM-level normalization in MaxQuant strongly improve reporter ion-based quantification - mouse tissue dataset
Isobaric labeling has the promise of combining high sample multiplexing with precise quantification. However, normalization issues and the missing value problem of complete n-plexes hamper quantification across more than one n-plex. Here we applied two novel algorithms implemented in MaxQuant that s...
ORGANISM(S): Mus musculus (Mouse) 
2020-06-22 | PXD019880 | Pride
Match between runs Normalization Tandem mass tag Isobaric labeling Multiplexed quantification 
ProteomicsIsobaric matching between runs and novel PSM-level normalization in MaxQuant strongly improve reporter ion-based quantification - Peli1 knock-out mice dataset
Isobaric labeling has the promise of combining high sample multiplexing with precise quantification. However, normalization issues and the missing value problem of complete n-plexes hamper quantification across more than one n-plex. Here we introduce two novel algorithms implemented in MaxQuant that...
ORGANISM(S): Mus musculus (Mouse) 
2020-06-22 | PXD019881 | Pride
Match between runs Normalization Tandem mass tag Isobaric labeling Multiplexed quantification 
ProteomicsTowards optimised extracellular vesicle proteomics from cerebrospinal fluid
The proteomic profile of extracellular vesicles (EVs) from cerebrospinal fluid (CSF) can reveal novel biomarkers for diseases of the brain. Here, we validate an ultrafiltration combined with size-exclusion chromatography (UF-SEC) method for isolation of EVs from canine CSF and probed the effect of s...
ORGANISM(S): Canis familiaris (Dog) (Canis lupus familiaris) 
2023-07-20 | PXD036748 | Pride
Proteomics Ultrafiltration combined with size-exclusion chromatography Extracellular vesicles Cerebrospinal fluid 
ProteomicsSystems biology of blood and tissue for comprehensive analysis of immune response to hepatitis B vaccine in adults
Protein concentrations of both lysed WBC and plasma samples were measured by the PierceTM Bradford Assay and normalized to contain 10 μg per sample before proceeding with sample digestion using the procedure as previously described44. Peptides were desalted using STop-And-Go Extraction tips (STAGE t...
ORGANISM(S): Homo sapiens (Human) 
2020-12-01 | PXD020474 | Pride
Tissue Blood Systems biology Hepatitis b vaccone 
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