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MetabolomicsComprehensive evaluation of untargeted metabolomics data processing software in feature detection, quantification and discriminating marker selection (AB SCIEX TripleTOF 6600 assay)

Data analysis represents a key challenge for untargeted metabolomics studies and it commonly requires extensive processing of more than thousands of metabolite peaks included in raw high-resolution MS data. Although a number of software packages have been developed to facilitate untargeted data p...

2019-11-19 | MTBLS736 | MetaboLights
MetabolomicsComprehensive evaluation of untargeted metabolomics data processing software in feature detection, quantification and discriminating marker selection
Data analysis represents a key challenge for untargeted metabolomics studies and it commonly requires extensive processing of more than thousands of metabolite peaks included in raw high-resolution MS data. Although a number of software packages have been developed to facilitate untargeted data proc...
2019-11-19 | MTBLS733 | MetaboLights
ProteomicsCombining Untargeted and Targeted Proteomic Strategies for Discrimination and Quantification of Cashmere Fibers
Cashmere is regarded as a specialty and luxury fiber due to its scarcity and high economic value. For fiber quality assessment, it is technically very challenging to distinguish and quantify the cashmere fiber from yak or wool fibers because of their highly similar physical appearance and substantial...
ORGANISM(S): Bos mutus grunniens (Wild yak) (Bos grunniens) Ovis aries Capra hircus (Goat) 
2018-10-25 | PXD003107 | Pride
Keratin-associated protein Proteomics Lc-ms Fiber Keratin Biomarker 
MetabolomicsPlant elicitor peptide signalling confers rice resistance to piercing-sucking insect herbivores and pathogens
Rice is a staple food crop worldwide, and its production is severely threatened by phloem-feeding insect herbivores, particularly the brown planthopper (BPH, Nilaparvata lugens), and destructive pathogens. Despite the identification of many BPH resistance genes, the molecular basis of rice resistanc...
2022-02-23 | MTBLS3518 | MetaboLights
ProteomicsDeepPhospho generated libraries, search results, models, and synthetic data
In this study, we present a hybrid deep neural network DeepPhospho which conceptually differs from all previous deep learning models for unmodified or modified peptide predictions in regard to peptide representation learning. Our approach utilizes a multi-module network and self attention mechanism ...
ORGANISM(S): Homo Sapiens 
PXD028601 |
ProteomicsProteome-wide identification of SAPs in an industrial yeast strain
Most proteogenomic approaches for mapping single amino acid polymorphisms (SAPs) require construction of a sample-specific database containing protein variants predicted from the next-generation sequencing (NGS) data. We present a new strategy for direct SAP detection without relying on NGS data. Am...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2018-04-18 | PXD003101 | Pride
Industrial yeast strain Proteogenomics Sap 
ProteomicsBenchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics
This repository is related to the work "Benchmarking commonly usedsoftware suites and analysis workflows for DIA proteomics and phosphoproteomics". The following files are stored here: 1. four MS datasets generated in this work, including two two-species benchmark datasets acquired on QE HF and tims...
ORGANISM(S): Homo Sapiens Saccharomyces Cerevisiae S288c Mus Musculus 
2022-12-08 | PXD034709 |
UnknownThe genome draft of coconut (Cocos nucifera).
Not available
S-EPMC5714197 | biostudies-literature
ProteomicsGeneration of a deep mouse brain spectral library for transmembrane proteome profiling in mental disease models
The establishment of a high-quality mouse brain transmembrane proteins spectral library enables in-depth profiling of the proteins across multiple brain regions. DIA data analysis, combining different search pipeline based on the spectral library, discovered a new GPCR regulator which was associated...
ORGANISM(S): Mus Musculus 
2023-11-26 | PXD047251 |
ProteomicsMouse brain tissue proteomics-Shui group
DIA and PRM raw data of mouse brain tissues. R1: Cerebellum, R2: Midbrain, R3: Spinal cord
ORGANISM(S): Mus Musculus 
2019-11-26 | PXD016441 |
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