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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 |
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 
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 
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 
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 
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 
ProteomicsStructural aspects of FOXO4 binding to DAF16 investigated with FPOP using both bottom-up and top-down MS.
A combination of covalent labelling techniques and mass spectrometry (MS) is currently a progressive approach for the de-riving insights relating to the mapping of protein surfaces or protein-ligand interactions. In this study, we mapped an interac-tion interface between DNA binding domain (DBD) of ...
ORGANISM(S): Homo sapiens (Human) 
2022-02-14 | PXD027624 | Pride
Bottom-up proteomics Dna Transcription factors Protein Foxo4 Fast photochemical oxidation of proteins Top-dow proteomics 
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 
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 
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