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ProteomicsDetergent Screening with Hybrid Detergents Increases Observable Number of Protein Identities in Bottom-Up Proteomics
Detergents are key reagents in bottom-up proteomics that create an apparent, yet underappreciated bias on observable proteomes. Maximizing the chemical diversity in parallelized detergent screens is supposed to maximize observable proteomes by combining proteomics data sets of different detergents. ...
ORGANISM(S): Escherichia coli 
2025-08-25 | PXD060875 | Pride
Proteomics E. coli Bottum-up Hybrid detergent Sds 
ProteomicsExtending the coverage of Lys-C/trypsin-based bottom-up proteomics using cysteine S-aminoethylation
In this study, S-aminoethylation of Cys (AE-Cys) was carried out with 2-bromoethylamine to form pseudo-Lys, which was then digested with Lys-C or trypsin to improve proteome coverage in bottom-up proteomics. A model study with bovine serum albumin showed that the C-terminal side of Cys was successfu...
ORGANISM(S): Homo Sapiens (human) Bos Taurus 
2023-09-27 | PXD045433 | JPOST Repository
ProteomicsSuspension trapping (S-trap) is compatible with typical protein extraction buffers and detergents for bottom up proteomics
Analysis of cells and tissue by bottom up proteomics starts with lysis, followed by in-solution digestion. Lysis buffers commonly used include detergents and other reagents for efficient solubility of the proteins. However these reagents are, for the most part, incompatible with downstream analytica...
ORGANISM(S): Homo sapiens (Human) 
2019-02-28 | PXD011665 | Pride
Q eaxctive hf Lysis Proteomics Hela S-trap 
ProteomicsSolid phase microextraction-aided capillary zone electrophoresis-mass spectrometry: ready for bottom-up proteomics of single human cells
Capillary zone electrophoresis-mass spectrometry (CZE-MS) has been recognized as a valuable technique for proteomics of mass-limited biological samples (i.e., single cells) due to its high efficiency and high sensitivity for peptide separation and detection. However, its broad adoption for single ce...
ORGANISM(S): Homo sapiens (Human) 
2024-05-01 | PXD047627 | Pride
Hela Single cell proteomics Mass limited Solid phase microextraction Mass spectrometry Bottom-up proteomics 
ProteomicsSulfolobus islandicus HCD+ETD, including LFQ
Protein posttranslational methylation and acetylations have been reported to occur in archaea, including members of the genus Sulfolobus, but have not been characterized on a proteome-wide scale. Sulfolobus chromatin proteins are known to be methylated and acetylated on lysine side chains, resemblin...
ORGANISM(S): Sulfolobus islandicus LAL14/1 
2022-03-01 | PXD003102 | Pride
Strong cation exchange Archaea Hcd Label-free quantitation Etd Sulfolobus islandicus 
ProteomicsSimple Strategy of Integrating the Micro-centrifugation-based Extraction and 4-Hexylphenylazosulfonate for the Preparation of Plant Microsomal Proteins for Bottom-Up Proteomics
The preparation of high-quality microsomal proteins (MPs) is of critical importance to high-throughput microsomal proteomics. The isolation of MPs for proteomic analysis has to date relied on Ultracentrifugation-based methods (UBMs), however, these methods are labor-intensive, time-consuming, and un...
ORGANISM(S): Oryza sativa subsp. japonica (Rice) 
2021-09-29 | PXD025132 | Pride
Rice leaves Perseus Label-free quantitative proteomics Ultracentrifugation Micro-centrifugation Azo Maxquant Microsomal membrane extraction Plasma membrane Sds 
ProteomicsThromboxane-A Synthase 1 as a Potential Dual Biomarker for Metastatic Prostate Cancer and Atherosclerosis: Insights from a Nanomedicine Protein Corona, Machine Learning, and Actual Causality Approaches
Prostate cancer (PC) is the most common cancer among men in the United States, while atherosclerosis (ASCVD) is the most prevalent cardiovascular disease (CVD) associated with it. CVD, particularly ASCVD, has been shown to contribute to metastatic prostate cancer (mPC) progression. Identifying blood...
ORGANISM(S): Homo sapiens (Human) 
2025-11-21 | PXD057863 | Pride
Protein corona Bottom up proteomics Machin learning Human plasma 
ProteomicsInteractome analyses reveal profound proteasome structural and functional rearrangements throughout mammalian spermatogenesis
Bottom-up, top-down proteomics and HDX-MS analysis of spermatoproteasome immunopurified from bovin testes and/or rat germ cells.
ORGANISM(S): Bos taurus (Bovine) Rattus norvegicus (Rat) 
2022-04-07 | PXD027436 | Pride
Proteasome Hydrogen-deuterium exchange Top-down proteomics Bottom-up proteomics Spermatoproteasome 
ProteomicsLabel-Free Quantitative Proteomics of Stallion Seminal Plasma Reveals Oxidative Stress–Associated Protein Signatures Linked to Sperm Motility and Viability
Seminal plasma proteins play critical roles in sperm function, motility, viability and oxidative stress regulation in stallions. In this study, label-free quantitative (LFQ) proteomics was applied to characterize seminal plasma protein signatures associated with sperm quality in Arabian stallions. S...
ORGANISM(S): Equus caballus (Horse) 
2026-05-25 | PXD078825 | Pride
Proteomics Sperm motility Seminal plasma Mitochondrial dysfunction Lfq Oxidative stress Stallion Casa 
ProteomicsProteome-wide evaluation of two common protein quantification methods
Proteomics experiments commonly aim to estimate and detect differential abundance across all expressed proteins. Within this experimental design, some of the most challenging measurements are small fold changes for lower abundance proteins. While bottom-up proteomics methods are approaching comprehe...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2018-04-05 | PXD007683 | Pride
Tmt Lfq Maxquant 
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