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TranscriptomicsComparison of Hi-C results using in-solution versus in-nucleus ligation
Chromosome conformation capture (3C) and derivative (4C, 5C and Hi-C) methods employ ligation of diluted cross-linked chromatin complexes, intended to favor proximity-dependent, intra-complex ligation. We previously described an alternative Hi-C protocol with ligation in preserved nuclei rather than...
ORGANISM(S): Mus musculus 
2015-08-12 | E-GEOD-70181 | biostudies-arrayexpress
ProteomicsDietary protein in vitro digest (LC-MS)
16 dietary protein preparations were digested according to a standardized invitro digestion (InfoGest) protocol, simulating gastrointestinal digestion. Resulting oligopeptide mixtures were subsequently analyzed by UPLC-MS using DDA shot-gun detection. Peak intensity data from MS1 spectra were obtain...
ORGANISM(S): Bos taurus (Bovine) Pisum sativum (Garden pea) Solanum tuberosum (Potato) Zea mays (Maize) Triticum aestivum (Wheat) Saccharomyces cerevisiae (Baker's yeast) Gallus gallus (Chicken) 
2021-09-09 | PXD021577 | Pride
Dietary protein  in vitro digest  lc-ms  de novo 
ProteomicsComplementary metaproteomic approaches to assess marine bacteriopankton response towards algal bloom
In this project, the metaproteome of the marine bacterioplankton was analyzed to assess its respone towards an algal bloom in the southern North Sea in spring 2010. Proteins were extracted applying two different methods: (i) applying chemical cell lysis using trifluoroethanol in combination with in-...
ORGANISM(S): environmental samples 
2017-04-11 | PXD004944 | Pride
Metaproteome Algal bloom Marine bacterioplankton 
ProteomicsHighly Multiplex Targeted Proteomics Enabled by Real-Time Chromatographic Alignment
Targeted mass spectrometry methods produce high quality quantitative data in terms of limits of detection and dynamic range, at the cost of a substantial compromise in throughput compared to methods such as data independent and data de-pendent acquisition. The logistical and experimental issues inhe...
ORGANISM(S): Homo Sapiens 
2021-01-24 | PXD018675 | panorama
ProteomicsUnified workflow for the rapid and in-depth characterization of bacterial proteomes
Among the kingdoms of life, bacteria are by far the most abundant, but also the most diverse organisms. Due to this excessive diversity, finding a unified, comprehensive and safe workflow for quantitative bacterial proteomics is highly challenging. In this study, we have systematically evaluated and...
ORGANISM(S): Bacillus Subtilis (ncbitaxon:1423) Enterococcus Faecalis (ncbitaxon:1351) Vibrio Proteolyticus (ncbitaxon:671) Lactobacillus Delbrueckii (ncbitaxon:1584) Burkholderia Cepacia (ncbitaxon:292) Streptococcus Mitis (ncbitaxon:28037) Staphylococcus Aureus (ncbitaxon:1280) Escherichia Coli (ncbitaxon:562) Bifidobacterium Bifidum (ncbitaxon:1681) Sphingobacterium Spiritivorum (ncbitaxon:258) Deinococcus Radiodurans (ncbitaxon:1299) Prevotella Melaninogenica (ncbitaxon:28132) Micrococcus Luteus (ncbitaxon:1270) Cutibacterium Acnes (ncbitaxon:1747) Brevundimonas Diminuta (ncbitaxon:293) Pseudomonas Aeruginosa (ncbitaxon:287) Anoxybacillus Flavithermus (ncbitaxon:33934) Acetobacter Aceti (ncbitaxon:435) Mycolicibacterium Smegmatis (ncbitaxon:1772) Listeria Monocytogenes (ncbitaxon:1639) Clostridium Sporogenes (ncbitaxon:1509) Bacillus Cereus (ncbitaxon:1396) Corynebacterium Glutamicum (ncbitaxon:1718) 
2023-01-18 | MSV000091088 | MassIVE
UnknownInvestigation of Tryptic Protein Digestion in Microdroplets and in Bulk Solution.
Not available
S-EPMC10512443 | biostudies-literature
UnknownSurface-Confined Aqueous Reversible Addition-Fragmentation Chain Transfer (SCARAFT) Polymerization Method for Preparation of Coated Capillary Leads to over 10 000 Peptides Identified from 25 ng HeLa Digest by Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry.
Not available
S-EPMC5540315 | biostudies-literature
ProteomicsIntact Transition Epitope Mapping- Thermodynamic Weak-force Order (ITEM-TWO)
Most important characteristics of antibodies are that they typically strongly bind to specific epitopes, thereby expressing low dissociation constants (KDs) and high Gibbs free binding energies (delta Gs). In this study, we describe an off-line nano-electrospray mass spectrometry method, termed IT...
ORGANISM(S): Homo sapiens (Human) 
2019-11-07 | PXD016024 | Pride
Antibody affinity determination Antibody specificity determination 
ProteomicsProteomic and unbiased post-translational modification profiling of amyloid plaques and surrounding tissue in a transgenic mouse model of Alzheimer’s disease
Amyloid plaques (Aβ plaques) are one of the hallmarks of Alzheimer’s disease (AD). The main constituent of Aβ plaques is beta-amyloid peptides but a complex interplay of other infiltrating proteins also co-localizes. We focused on proteomic differences between Aβ plaques and adjacent control tissue ...
ORGANISM(S): Mus musculus (Mouse) 
2021-03-25 | PXD014274 | Pride
Amyloid plaque Alzheimer’s disease Mass spectrometry Post transcriptional modifications Laser capture microdissection 
ProteomicsIn-Depth Comparison of Reagent-Based Digestion Methods and Two Commercially Available Kits for Bottom-Up Proteomics
We assessed two physical disruption methods to homogenize cells —sonication and BeatBox—alongside four digestion protocols. Two of them are lab-reagent strategies: urea-based, and SDC (Sodium deoxycholate)-based in-solution digestion, and two are commercially available kits: the EasyPep kit from The...
ORGANISM(S): Homo sapiens (Human) 
2026-01-07 | PXD056409 | Pride
In-solution digestion Lc-ms Proteomics Proteolysis Bottom-up proteomics 
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