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ProteomicsNickel Binding- and Histidine-Rich Proteins of Helicobacter species
The files in this archive examine six species within the genus Helicobacter to assay their histidine-rich proteins. They correspond to the manuscript "Expansion of nickel binding- and histidine-rich proteins during gastric adaptation of Helicobacter species" by Frederic Fischer, Egor Vorontsov, Eve...
ORGANISM(S): Helicobacter Felis (ncbitaxon:214) Helicobacter Bizzozeronii (ncbitaxon:56877) Helicobacter Pylori (ncbitaxon:210) Helicobacter Acinonychis (ncbitaxon:212) Helicobacter Mustelae (ncbitaxon:217) Helicobacter Hepaticus (ncbitaxon:32025) 
2022-03-23 | MSV000089106 | MassIVE
ProteomicsTDFragMapper: Evaluating experimental parameters for confident intact protein characterization in top-down proteomics
New software-tool allowing an easy visualization of fragment ions and thus a rapid evaluation of key experimental parameters on the sequence coverage obtained for the MS/MS analysis of intact proteins. Our tool can deal with multiple fragmentation methods. We demonstrate that TDFragMapper can rapidl...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Streptococcus dysgalactiae Escherichia coli 
2021-12-30 | PXD024643 | Pride
Visualization tool Top-down proteomics Lc-ms/ms 
ProteomicsA multi-parameter optimization in middle-down analysis of monoclonal antibodies by LC-MS/MS
In antibody-based drug research, regulatory agencies request a complete characterization of antibody proteoforms covering both the amino acid sequence and all post-translational modifications. The usual mass spectrometry-based approach to achieve this goal is bottom-up proteomics, which relies on th...
ORGANISM(S): Homo sapiens (Human) 
2023-03-15 | PXD038619 | Pride
Orbitrap ms Middle-down proteomics Monoclonal antibody Intact proteins Lc-ms/ms 
ProteomicseXL-MS: An enhanced Cross-Linking Mass Spectrometry Workflow to Study Protein Complexes.
The analysis of proteins and protein complexes by cross-linking mass spectrometry (XL-MS) has expanded in the last dec-ade. However, mostly used approaches suffer important limitations in term of efficiency and sensitivity. We describe here a new workflow based on the advanced use of the trifunction...
ORGANISM(S): Oryctolagus cuniculus (Rabbit) 
2021-08-11 | PXD010422 | Pride
Creatine kinase Mass spectrometry Cross-link Monoavidin biotin affinty enrichment Click chemistry 
ProteomicsOptimization of a Top-Down Proteomics Platform for Closely-Related Pathogenic Bacteria Discrimination
The current technique used for microbial identification in hospitals is MALDI-TOF MS. However, it suffers from important limitations, in particular for closely-related species or when the database used for the identification lacks the appropriate reference. In this work, we set up a high throughput ...
ORGANISM(S): Shigella flexneri Salmonella enterica subsp. enterica serovar Muenchen Salmonella enterica subsp. enterica serovar Enteritidis Salmonella enterica subsp. enterica serovar Typhimurium Escherichia coli O26:H11 Shigella sonnei Escherichia coli O157:H7 Salmonella enterica subsp. enterica serovar Newport Escherichia coli 
2020-09-24 | PXD019247 | Pride
Mass spectrometry Optimization Top-down proteomics Bacteria 
UnknownIR action spectroscopy shows competitive oxazolone and diketopiperazine formation in peptides depends on peptide length and identity of terminal residue in the departing fragment.
Not available
S-EPMC6467643 | biostudies-literature
ProteomicsSulfolobus islandicus top-down LC-MSMS
Protein posttranslational methylation and acetylations have been reported to occur in archaea, including members of the genus Sulfolobus, but have not been characterized on a proteome-wide scale. Sulfolobus chromatin proteins are known to be methylated and acetylated on lysine side chains, resemblin...
ORGANISM(S): Sulfolobus islandicus LAL14/1 
2016-09-13 | PXD003074 | Pride
Archaea Top-down Lc-msms Orbitrap fusion 
ProteomicsMounting, structure and autocleavage of a type VI secretion-associated Rhs polymorphic toxin
Bacteria have evolved effectors or toxins to outcompete other bacteria or to hijack host cell pathways. One broad family of bacterial polymorphic toxins regroups multidomain proteins with a modular organization, that comprise a C-terminal toxin domain fused to a N-terminal domain that adapt to the d...
ORGANISM(S): Escherichia coli Bacteria 
2021-11-30 | PXD028652 | Pride
Re-arrangement hot spot Spike Cross-linking Polymorphic toxin Β-roll Chaperone Autocleavage Vgrg Architecture 
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 
ProteomicsMonitoring mAb proteoforms in mouse plasma using an automated immunocapture combined with top-down and middle-down mass spectrometry
We propose here a workflow based on an automated immunocapture followed by top-down and middle-down LC-MS/MS approaches to characterize mAb proteoforms spiked in mouse plasma. We demonstrate the applicability of our workflow on a large concentration range using pembrolizumab as a model. We also comp...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2024-08-27 | PXD040896 | Pride
Immunocapture Monoclonal antibody Proteoforms Middle-down mass spectrometry Top-down mass spectrometry 
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