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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 
TranscriptomicsInduction of a peptide with activity against a broad spectrum of pathogens in the Aedes aegypti salivary gland, following infection with dengue virus
Dengue viruses (DENV) are generally maintained in a cycle which requires horizontal transmission via their arthropod vector, Ae. Aegypti, to the vertebrate host. One important consequence of this process is the interference of these arboviruses with both invertebrate and vertebrate immune systems. W...
ORGANISM(S): Aedes aegypti 
2011-03-21 | E-GEOD-21528 | biostudies-arrayexpress
UnknownA peptide filtering relation quantifies MHC class I peptide optimization.
Not available
S-EPMC3195949 | biostudies-literature
TranscriptomicsTranscription profiling of human glucose-dependent insulinotropic peptide (GIP)- and adrenocorticotropin-dependent adrenal hyperplasias reveals novel targets for the study of GIP-dependent Cushings syndrome.
The mechanisms responsible for the ectopic adrenal expression of glucose-dependent insulinotropic peptide (GIP) receptor (GIPR) in GIP-dependent Cushing's syndrome (CS) are unknown. Chronic adrenal stimulation by ACTH in Cushing's disease or GIP in GIP-dependent ACTH-independent macronodular adrenal...
ORGANISM(S): Homo sapiens 
2007-10-02 | E-GEOD-4060 | biostudies-arrayexpress
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
UnknownSTEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results.
Not available
S-EPMC3676282 | biostudies-literature
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 
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 
UnknownIDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.
Not available
S-EPMC2810655 | biostudies-literature
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