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ProteomicsPeptide Filtering and Quantification Methods
In bottom-up proteomics, data are acquired on peptides resulting from proteolysis. In XIC-based quantification, the quality of the protein abundance estimation depends on how peptide data are filtered and on which quantification method is used to sum up peptide intensities into protein abundances. S...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2018-11-14 | PXD009740 | Pride
Peptide filtering Quantification methods Extracted ion current 
ProteomicsMaxQuant.Live enables enhanced selectivity and identification of peptides modified by endogenous SUMO and ubiquitin
Small ubiquitin-like modifiers (SUMOs) and ubiquitin are frequent post-translational modifications of proteins that play pivotal roles in all cellular processes. We previously reported mass spectrometry-based proteomics methods that enable profiling of lysines modified by endogenous SUMO or ubiquiti...
ORGANISM(S): Homo sapiens (Human) 
2021-02-05 | PXD022367 | Pride
Peptide mass filtering Sumo Mql Ubiquitin Maxquant.live Precursor untargeting 
ProteomicsIsobaricQuant enables cross-platform quantification, visualization, and filtering of isobarically-labeled peptides
In mass spectrometry (MS)-based quantitative proteomics, labeling with isobaric mass tags such as iTRAQ and TMT can substantially improve sample throughput and reduce peptide missing values. Nonetheless, the quantification of labeled peptides tends to suffer from reduced quantitative accuracy due to...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2022-07-11 | PXD034534 | Pride
Reanalysis 
TranscriptomicsTargeting MDM4/MDM2 binding interface for reactivation of p53 in cancer therapy
The aim of this experiment has been to investigate the transcriptional profile of HCT116 cells treated with Peptide-3 (Pep3) compared to untreated (NT), treated with solvent (DMSO) or with a mutated peptide (Pep3M) cells. Peptide-3 is a dodecapeptide able to interact with MDM2 at the levels of the i...
ORGANISM(S): Homo sapiens 
2017-04-18 | E-GEOD-62855 | biostudies-arrayexpress
UnknownPredicting peptide properties from mass spectrometry data using deep attention-based multitask network and uncertainty quantification.
Not available
S-EPMC11370541 | biostudies-literature
UnknownIDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.
Not available
S-EPMC2810655 | biostudies-literature
ProteomicsProteogenomics of malignant melanoma cell lines: searching for genetically encoded point mutations in LC-MS/MS data
In this study we performed proteogenomic analysis for 9 cell lines of malignant melanoma. The main objectives of the study were identifying the variants originating from point mutations and analyzing the effect of exome data filtering on the outcome of variant identification.
ORGANISM(S): Homo sapiens (Human) 
2018-12-05 | PXD007662 | Pride
Ls-ms/ms Melanoma 
ProteomicsSynthetic peptide library
Synthetic peptides are commonly used in biomedical science for many applications in basic and translational research. Here, we assembled a large dataset of synthetic peptides whose identity was validated using mass spectrometry. We analyzed the mass spectra and used them for method validation as wel...
ORGANISM(S): Homo sapiens (Human) 
2022-10-11 | PXD031812 | Pride
Peptide synthesis Mass spectrometry Predictor 
UnknownIsobaricQuant enables cross-platform quantification, visualization, and filtering of isobarically-labeled peptides.
Not available
S-EPMC9894126 | biostudies-literature
TranscriptomicsMicroarray of isolated adipocytes from subcutaneous adipose tissue of severely obese patients compared to lean controls
The aim of the project was to compare global gene expression in adipocytes from obese patients and lean controls. Subcutaneous adipose tissue was collected from severely obese patients undergoing bariatric surgery (average body-mass index (BMI) of 45.5 kg/m2 (n = 12, thereof 4 men) and healthy lean...
ORGANISM(S): Homo sapiens 
2018-12-12 | E-MTAB-6728 | biostudies-arrayexpress
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