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UnknownMSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale.
Not available
S-EPMC10629259 | biostudies-literature
ProteomicsMSstats splitplot method for protein quantitation in MS datasets
Thirty commercial proteins were prepared at 1.5 pmol/µL in three different subsets of 10 proteins each. Proteins from these subsets were spiked to a 15-µg Escherichia coli background in different amounts and five different mixtures were prepared in triplicates. The final amount of each protein in ea...
ORGANISM(S): Escherichia coli 
2019-07-19 | PXD005642 | Pride
Statistics Proteomics Msstats Mass spectrometry 
ProteomicsDIA Quantification Proteomics of rat tissues including bph and sham rats
In this project, Q-Exactive HF(Thermo Fisher Scientific,San Jose,CA) was used to acquire mass spectrometry (MS) data for 7 samples in Data Independent Acquisition (DIA) mode. Quantification of peptides and proteins was performed using Spectronaut™ and MSstats software packages
ORGANISM(S): Rattus norvegicus (Rat) 
2025-12-01 | PXD032395 | Pride
Lc-msms Prostate Rats 
ProteomicsAccounting for longitudinal peak quality metrics with MSstats+ enhances differential analysis in proteomic experiments with data-independent acquisition
Mass spectrometry-based proteomics with data-independent acquisition benefits from advanced instrumentation and computational analysis. Despite continued im- provements, the quality of quantification may be poor for some measurements. As the scale of proteomic experiments increases, these poor-quali...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2025-07-23 | MSV000098622 | MassIVE
ProteomicsIdentification of the protein interaction network of Stag proteins
This study involves the identification of specific Stag1 interactors with and without Cohesin loss. Stag1 was immunoprecipiated from human HCT116 cells, under 4 treatments - untreated (UTR), Non-specific siRNA treatment (SiCON), SA1 siRNA treatment (SiSA1) and Auxin treatment for Cohesin loss (IAA)....
ORGANISM(S): Homo sapiens (Human) 
2023-04-18 | PXD024354 | Pride
Human Ap-ms Lc-ms Lfq Stag 
ProteomicsIdentification of the protein interaction network of STAG2 protein isoforms with inclusion and exclusion of exon32
This study involves the identification of specific interactors for STAG2ex32+ and STAG2ex32delta. Plasmids expressing YFP-STAG2 isoforms were transfected into HCT116OsTIR cells using untransfected cells as mock control. 40h post transfection, whole cell lysates were extracted and STAG2 isoforms were...
ORGANISM(S): Homo sapiens (Human) 
2023-05-04 | PXD041975 | Pride
Ap-ms 
ProteomicsProteomic analysis of vascular tissue from critical limb ischemia mouse models treated with Etrinabdione
Vasculogenic therapies have been investigated for the treatment of peripheral artery disease (PAD) with very limited success in clinical trials. The isoform PP2A (protein phosphatase 2)/B55alpha inhibits the activity of the prolyl hydroxylase 2 (PHD2) and activates the hypoxia inducing factor-1alpha...
ORGANISM(S): Mus musculus (Mouse) 
2024-04-03 | PXD050360 | Pride
Vascular tissue Critical limb ischemia 
ProteomicsData Independent Acquisition (DIA) based quantification workflow for proteome analysis of GASH/Sal and Control hamster
The GASH/Sal hamster (Genetic audiogenic seizure, Salamanca) is a model of audiogenic seizures with the epileptogenic focus localized in the inferior colliculus (IC). The sound-induced seizures exhibit a short latency (7-9 seconds), which implies innate protein disturbances in the IC as a basis for ...
ORGANISM(S): Mesocricetus auratus (Golden hamster) 
2023-05-10 | PXD039755 | Pride
Maxquant Msstats Dia Dda Mprophet 
UnknownDetecting differential protein abundance by combining peptide level P-values.
Not available
S-EPMC9514008 | biostudies-literature
UnknownSWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.
Not available
S-EPMC4824525 | biostudies-literature
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