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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 
2023-04-03 | PXD041291 |
ProteomicsCharacterization of human sperm protamine proteoforms through a combination of top-down and bottom-up mass spectrometry approaches
Protamine 1 (P1) and protamine 2 family (P2) are the most abundant nuclear basic spermspecific proteins, packing 85-95% of the paternal DNA. P1 is synthesized as a mature form, whereas P2 components (HP2, HP3 and HP4) arise from the proteolysis of the precursor (pre-P2). Due to the particular protam...
ORGANISM(S): Homo sapiens (Human) 
2019-11-11 | PXD014618 | Pride
Protamines  sperm  post-translational modifications  phosphorylation  nonannotated proteins  male infertility. Top-down proteomics  bottom-up proteomics  proteoforms  electron transfer dissociation 
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 
UnknownPressurized pepsin digestion in proteomics: an automatable alternative to trypsin for integrated top-down bottom-up proteomics.
Not available
S-EPMC3033671 | biostudies-literature
ProteomicsAn improved nanoflow RPLC-CZE-MS/MS system with high peak capacity and sensitivity for nanogram bottom-up proteomics
Novel mass spectrometry (MS)-based proteomic tools with extremely high sensitivity and high peak capacity are required for comprehensive characterization of protein molecules in mass-limited proteome samples. We previously reported a nanoflow RPLC-CZE-MS/MS (nanoRPLC-CZE-MS/MS) system for deep botto...
ORGANISM(S): Homo sapiens (Human) 
2019-10-23 | PXD014392 | Pride
Human cells Nanorplc-cze-ms/ms Bottom-up proteomics Nanograms 
ProteomicsHydrophobic interaction chromatography for bottom-up proteomics
Hydrophobic interaction chromatography as a first dimension to reduce samples complexity for bottom-up proteomics analyses of single proteins and protein complexes
ORGANISM(S): Homo sapiens (Human) 
2017-05-16 | PXD006217 | Pride
Lc-ms/ms  hic  human 
ProteomicsDifferential bottom-up proteomics of truffles
To compare truffles on protein level, samples of different truffle species (T. magnatum, T. indicum, T. melanosporum, T. aestivum and T. albidum Pico) were analysed by a LC-MS/MS based shotgun proteomics approach. First, different established bottom-up proteomics sample preparation approaches for in...
ORGANISM(S): Tuber aestivum Tuber magnatum Tuber albidum Tuber indicum Tuber melanosporum Mel28 
2021-12-19 | PXD027871 | Pride
Dia Lc-ms Truffles 
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 
UnknownSystematic Evaluation of Immobilized Trypsin-Based Fast Protein Digestion for Deep and High-Throughput Bottom-Up Proteomics.
Not available
S-EPMC5932237 | biostudies-literature
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