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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 
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 
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 
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 
ProteomicsTCUP: Typing and characterization of bacteria using bottom-up tandem mass spectrometry proteomics
Methods for rapid and reliable microbial identification are essential in modern healthcare. The ability to detect and correctly identify pathogenic species and their resistance phenotype is necessary for accurate diagnosis and efficient treatment of infectious diseases. Bottom-up tandem mass spectro...
ORGANISM(S): Escherichia coli 
2017-04-20 | PXD004321 | Pride
Tandem mass spectrometry Bottom-up Proteotyping 
ProteomicsBottom-up and top-down LC-MS/MS of ribosomal purifications
Ribosomal purifications of spinach 70S ribosome and human 40S and 60S ribosomal subunits were analyzed with bottom-up LC-MS/MS to identify proteins comprising purified complexes as well as co-purified proteins. In order to assess and quantify proteoforms of ribosomal proteins in ribosomal purificati...
ORGANISM(S): Spinacia oleracea Homo sapiens (Human) Escherichia coli 
2018-06-26 | PXD008881 | Pride
Ribosome Top-down Bottom-up 
ProteomicsProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment
Here we present a high-performance software for proteome analysis that combines different mass spectrometric approaches, such as, top-down for intact protein analyses and both bottom-up and middle-down, for proteolytic fragment characterization.
ORGANISM(S): Escherichia coli 
2020-11-02 | PXD017618 | Pride
Bottom-up Bioinformatics Top-down 
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 
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 
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 
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