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ProteomicsModification localization and quality control for open database search results
Open (mass tolerant) search of tandem mass spectra shows great potential in the comprehensive detection of post-translational modifications in shotgun proteomics. However, this search strategy has not been widely used by the community, and one bottleneck of it is the lack of appropriate algorithms f...
ORGANISM(S): Homo Sapiens 
2019-01-17 | PXD012394 |
ProteomicsIdentification of Poly Ethylene Glycol (PEG) and PEG-based Detergents Using Peptide Search Engines
Polyethylene glycol (PEG) is one of the most common polymer contaminations in MS samples. At present, the detection of PEG and other polymers relies largely on manual inspection of raw data which is laborious and frequently difficult due to sample complexity and retention characteristics of polymer ...
ORGANISM(S): Rattus rattus (Black rat) 
2018-05-28 | PXD009376 | Pride
Automated Polymer Mass spectrometry Peptide search engine Peg Poly ethylene glycol 
UnknownA Computational Design Framework for Efficient, Fabrication Error-Tolerant, Planar THz Diffractive Optical Elements.
Not available
S-EPMC6456492 | biostudies-literature
ProteomicsSystematic Evaluation of Protein Reduction and Alkylation reveals Massive Unspecific Side Effects by Iodine-containing Reagents
In this study, we systematically evaluated reduction and alkylation of proteins using three reducing agents (DTT, TCEP, and BME) in combination with four alkylation agents (IAA, IAC, AA, and CAA). We tested these conditions using strong anion exchange (SAX) fractionated in-solution digests and in-ge...
ORGANISM(S): Homo sapiens (Human) 
2017-05-30 | PXD005183 | Pride
Alkylation Proteomics Reduction 
ProteomicsProteomics characterization of purified SARS-CoV-2 viral particles for search of mutations.
Shotgun proteomics characterization of purified SARS-CoV-2 viral particles and interpretation in error-tolerant mode.
ORGANISM(S): Severe acute respiratory syndrome coronavirus 2 
2021-05-31 | PXD025130 | Pride
Mass spectrometry Virus Proteomics Sars-cov-2 Variants Covid-19 Mutations 
ProteomicsHow processing affects marker peptide quantification – A comprehensive estimation on bovine material relevant for food and feed control
Processing food and feed challenges official control e.g. by modifying proteins, which leads to significant underestimation in targeted, MS-based protein quantification. Whereas numerous studies identified processing-induced changes on proteins in various combinations of matrices and processing cond...
ORGANISM(S): Bos taurus (Bovine) 
2025-06-05 | PXD047055 | Pride
Ruminant Error-tolerant search Processing Proteomics Mass spectrometry Marker Post-translational modification (ptm) Feed 
ProteomicshSWATH: Unlocking SWATH’s full potential for an untargeted histone perspective
Mass spectrometry (MS) has become the technique of choice for large-scale analysis of histone post-translational modifications (hPTMs) and their combinatorial patterns, especially in untargeted settings where novel discovery-driven hypotheses are being generated. However, MS-based histone analysis r...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2019-08-27 | PXD011198 | Pride
Sequential window acquisition of all theoretical fragment ion spectra (swath)  data independent acquisition (dia)  histone  mass spectrometry (ms)  post-translational modification (ptm)  epigenetics 
UnknownA New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs.
Not available
S-EPMC12324293 | biostudies-literature
ProteomicsTowards an upgraded honey bee (Apis mellifera L.) genome annotation using proteogenomics.
The honey bee is a key pollinator in many agricultural operations as well as a model organism for studying the genetics and evolution of social behaviour. The Apis mellifera genome has been sequenced and annotated twice over, enabling proteomics and functional genomics methods for probing relevant a...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) Apis mellifera (Honeybee) Drosophila melanogaster (Fruit fly) Saccharomyces cerevisiae (Baker's yeast) Caenorhabditis elegans 
2016-01-18 | PXD002275 | Pride
Honey bees Proteogenomics Mass spectrometry Gene annotation Apis mellifera 
ProteomicsProteomic insights into novel food insects: Homology-based proteome characterization and allergenicity considerations for EU-regulated insect species
Insects have emerged as a sustainable alternative protein source and recently gained regulatory approval in the European Union as novel foods and animal feed ingredients. However, the limited availability of species-specific proteomic databases presents a significant challenge for the accurate ident...
ORGANISM(S): Hermetia illucens Gryllodes sigillatus Acheta domesticus Alphitobius diaperinus Tenebrio molitor Locusta migratoria 
2025-06-03 | PXD061237 | Pride
Allergen Insect Lc-ms/ms 
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