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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 
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 |
UnknownIntegrated Bottom-Up and Top-Down Proteomics of Patient-Derived Breast Tumor Xenografts.
Not available
S-EPMC4762530 | biostudies-literature
ProteomicsBottom-up spatial proteomics MALDI MSI
New workflow for spatial bottom-up proteomics at single-cell resolution.
ORGANISM(S): Homo sapiens (Human) 
2025-05-07 | PXD056528 | Pride
Maldi msi Spatial proteomics 
ProteomicsIntegrated bottom-up and top-down proteomics of patient-derived breast tumor xenografts

Ntai, I., LeDuc, R.D., Fellers, R.T., et al., (2015) Molecular and Cellular Proteomics, Manuscript M114.047480

Bottom-up proteomics relies on the use of proteases and is the method ...

ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) 
2019-08-28 | MSV000084247 | MassIVE
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 
ProteomicsHigh Field Asymmetric Waveform Ion Mobility Spectrometry in Non-targeted Bottom-up Proteomics of Dried Blood Spot
Dried Blood Spots samples are a rich source of proteins and have therefore great potential for proteomics biomarker discovery studies. Only a few articles have used DBS samples for non-targeted bottom-up protein analysis, probably due to the complexity of the DBS samples. Gas-phase separation by ion...
ORGANISM(S): Homo sapiens (Human) 
2018-05-03 | PXD007926 | Pride
Faims Dried blood spot Non-targeted Bottom-up Proteomics 
ProteomicsIon mobility tandem mass spectrometry enhances performance of bottom-up proteomics
We describe a novel method utilizing ion mobility-based concentration of peptide fragment ions on a qTOF mass spectrometer improving the sensitivity of bottom-up proteomics by up to 10-fold. This enabled the identification of 7,500 human proteins within one day and 8,600 phosphorylation sites within...
ORGANISM(S): Homo sapiens (Human) 
2015-08-18 | PXD000863 | Pride
Quadrupole time of flight mass spectrometer Proteomics Ion mobility mass spectrometry Chemical proteomics Phosphoproteomics 
ProteomicsQualitative Analysis of short open reading frame encoded proteins from Methanosarcina mazei under stress conditions via bottom up and top down proteomics
In the present work we have analysed Methanosarcina mazei grown under different stressor conditions via combined top-down and bottom-up proteomic workflows to determine which SEP are differenitally present in responce to stress conditions
ORGANISM(S): Methanosarcina mazei Go1 
2024-09-24 | PXD055745 | Pride
Top-down proteomics Proteoforms Methanosarcina mazei 2d-lc-faims-ms/ms Bottom-up proteomics 
ProteomicsReversed-phase liquid chromatography of peptides for bottom-up proteomics: A tutorial
The data were recorded for a tutorial focused on reversed-phase liquid chromatography of peptides for bottom-up proteomics. The project does not have any biological/clinical relevance.
ORGANISM(S): Francisella tularensis subsp. holarctica FSC539 
2024-08-08 | PXD036783 | Pride
Method development  protein separation  tutorial Bottom-up proteomics  peptide separation  reversed-phase liquid chromatography  peptide properties 
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