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ProteomicsUniversal Solid-Phase Protein Preparation (USP3) for bottom-up and top-down proteomics
Selecting a sample preparation strategy for mass spectrometry-based proteomics is critical to the success of quantitative workflows. Here we present a universal, solid-phase protein preparation (USP3) method which is rapid, robust and scalable, facilitating high-throughput protein sample preparation...
ORGANISM(S): Homo sapiens (Human) 
2019-06-05 | PXD011169 | Pride
Top-down proteomics Universal solid-phase protein preparation Bottom-up proteomics Intact mass spectrometry 
ProteomicsQuantitative analsysis of short open reading frame encoded proteins from Methanosarcina mazei under stress conditions via bottom up proteomics
In the present work we have analysed Methanosarcina mazei grown under different stressor conditions via quantitative bottom-up proteomic workflows to determine which SEP are differenitally abundant in responce to stress conditions
ORGANISM(S): Methanosarcina mazei Go1 
2024-09-24 | PXD055748 | Pride
Quantitative bottom-up proteomics Methanosarcina mazei Lc-ms/ms 
ProteomicsDeep Bottom-up Proteomics Enabled by the Integration of Liquid-Phase Ion Trap
In this work, a LPIT-reversed phase liquid chromatography-tandem mass spectrometry (LPIT-RPLC-MS/MS) platform was established for deep bottom-up proteomics. LPIT was used here as a robust and effective method for peptide fractionation. LPIT separates peptides based on their effective charges and hyd...
ORGANISM(S): Homo Sapiens 
PXD041291 |
ProteomicsSulfolobus islandicus PTM and quantitative study using bottom-up proteomics
Protein posttranslational methylation and acetylation have been reported to occur in archaea, including the genus Sulfolobus, but have never been characterized on a proteome-wide scale. Among important Sulfolobus proteins carrying such modifications are the chromatin proteins that have been describe...
ORGANISM(S): Sulfolobus islandicus LAL14/1 Escherichia coli 
2016-09-13 | PXD004179 | Pride
Methylation Archaea Sulfolobus islandicus Label-free quantitation Orbitrap fusion Posttranslational modification 
ProteomicsRapid trypsin digestion at elevated temperature with calcium for enhanced bottom-up proteome analysis
Trypsin is frequently employed to cleave proteins ahead of mass spectrometry characterization. Traditionally, enzyme digestion involves overnight incubation of proteins at 37 °C, which is not only time consuming but can still yield in poor digestion efficiency. While raising the temperature should t...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) Bacteria 
2023-03-11 | PXD035682 | Pride
Trypsin  calcium  bottom-up proteomics  mass spectrometry  accelerated digestion  digestion efficiency  quantitative proteomics  sample preparation 
UnknownA shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics.
Not available
S-EPMC12577184 | biostudies-literature
ProteomicsImpact of Surfactants on Cumulative Trypsin Activity for Bottom-up Proteome Analysis
Detergents are often employed in bottom-up proteome workflows to maximize total proteome recovery, especially in the interest of membrane proteins. Conventionally, they are depleted prior to digestion, but recent works report enhanced proteolysis of membrane proteins by including denaturants across ...
ORGANISM(S): Bos taurus (Bovine) 
2024-04-23 | PXD050154 | Pride
Trypsin Bottom-up Digestion Quantitation Surfactants Proteomics 
UnknownApplication of targeted mass spectrometry in bottom-up proteomics for systems biology research.
Not available
S-EPMC6089676 | biostudies-literature
UnknownC-STrap Sample Preparation Method--In-Situ Cysteinyl Peptide Capture for Bottom-Up Proteomics Analysis in the STrap Format.
Not available
S-EPMC4583295 | biostudies-literature
UnknownPutting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?
Not available
S-EPMC8976764 | biostudies-literature
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