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MetabolomicsInhibition of anaerobic digestion by various ammonia sources resulted in subtle differences in metabolite dynamics

The impact of ammonia on anaerobic digestion performance and microbial dynamics has been extensively studied, but the concurrent effect of anions brought by ammonium salt should not be neglected. This paper studied this effect using metabolomics and a time-course statistical framework. Metabolomi...

2024-03-01 | MTBLS7859 | MetaboLights
MetabolomicsNew plasma preparation approach to enrich metabolome coverage in untargeted metabolomics: plasma protein bound hydrophobic metabolite release with proteinase K
Plasma untargeted metabolomics is a common method for evaluation of the mechanisms underlying human pathologies and identification of novel biomarkers. The plasma proteins provide the environment for transport of hydrophobic metabolites. The current sample preparation protocol relies on the immediat...
2022-03-18 | MTBLS670 | MetaboLights
ProteomicsEPURISp: Combining Enzymatic Digestion, Ultrafiltration, and Rapid In-situ Sample Purification for High-performance Proteomics
High-performance liquid tandem mass spectrometry (HPLC-MS) is widely employed for protein analysis in biological systems. However, conventional proteomic sample pre-treatment methods suffer from multiple steps and poor reproducibility. In this study, we introduce EPURISp (Enzymatic Digestion with Ul...
ORGANISM(S): Mus Musculus 
PXD044209 |
ProteomicsHit-Gel: Streamlining in-gel protein digestion for high-throughput proteomics experiments.
Traditional in gel-digestion procedures require extensive sample handling, are prone to contamination and not compatible with high-throughput sample preparation. To address these shortcomings, we have modified the conventional in-gel digestion procedure for high-throughput proteomics studies. The mo...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2018-10-16 | PXD009510 | Pride
Large-scale In-gel digestion Proteomics Tryptic digest Fractionation Native protein complex Sample preparation High-throughput Lc-ms/ms 
ProteomicsHit-Gel: Streamlining in-gel protein digestion for high-throughput proteomics experiments.
Traditional in gel-digestion procedures require extensive sample handling, are prone to contamination and not compatible with high-throughput sample preparation. To address these shortcomings, we have modified the conventional in-gel digestion procedure for high-throughput proteomics studies. The mo...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2018-10-16 | PXD009485 | Pride
Large-scale In-gel digestion Proteomics Tryptic digest Fractionation Native protein complex Sample preparation High-throughput Lc-ms/ms 
ProteomicsInfluence of digestion protocol in Protein Quantitation
Quantitative determination of absolute and relative protein amounts is an essential requirement for most current bottom-up proteomics applications, but protein quantitation estimates are affected by several sources of variability such as sample preparation, mass spectrometric acquisition, and data a...
ORGANISM(S): Escherichia coli 
2014-07-30 | PXD001187 | Pride
Protein quantitation Digestion protocols Fasp 
ProteomicsQuantitative assessment of the effects of trypsin digestion methods on immunoprecipitation-mass spectrometry-based protein-protein interaction analysis
Immunoprecipitation-mass spectrometry (IP-MS) has become the method of choice for discovering protein-protein interaction (PPI) under native conditions. The success of the IP-MS depends on the efficiency of trypsin digestion and recovery of the tryptic peptides for MS analysis. Several different pro...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) Homo sapiens (Human) 
2017-07-25 | PXD005984 | Pride
Rela interactome Trypsin digestion Protein-protein interaction 
ProteomicsQuantitative assessment of the effects of trypsin digestion methods on immunoprecipitation-mass spectrometry-based protein-protein interaction analysis - part2
Immunoprecipitation-mass spectrometry (IP-MS) has become the method of choice for discovering protein-protein interaction (PPI) under native conditions. The success of the IP-MS depends on the efficiency of trypsin digestion and recovery of the tryptic peptides for MS analysis. Several different pro...
ORGANISM(S): Homo sapiens (Human) 
2017-07-26 | PXD006739 | Pride
Protein-protein interaction Trypsin digestion Lc-ms/ms 
ProteomicsRefinement of paramagnetic bead–based digestion protocol for automatic sample preparation using an artificial neural network
Despite technological advances in the proteomics field, sample preparation still represents the main bottleneck in mass spectrometry (MS) analysis. Bead-based protein aggregation techniques have recently emerged as an efficient, reproducible, and high-throughput alternative for protein extraction an...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) Mus musculus (Mouse) Homo sapiens (Human) Escherichia coli Rattus norvegicus (Rat) 
2024-05-31 | PXD048358 | Pride
Bile Magnetic beads Protein aggregation Sp3 protein digestion Artificial neural network 
ProteomicsMassSpecPreppy - an end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics applications
In proteomics, fast, efficient and highly reproducible sample preparation are of utmost importance, particularly in view of fast scanning mass spectrometers enabling analyses of large sample series. To address this need, we have developed the web application MassSpecPreppy that operates on the open ...
ORGANISM(S): Saccharomyces Cerevisiae Strain C13-aby.s86 Escherichia Coli K-12 (ncbitaxon:83333) Homo Sapiens (ncbitaxon:9606) 
2023-07-20 | MSV000092489 | MassIVE
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