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MetabolomicsIntegration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance
The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. W...
2021-04-06 | MTBLS2021 | MetaboLights
ProteomicsLung proteomic biomarkers associated with chronic obstructive pulmonary disease
Identifying protein biomarkers for chronic obstructive pulmonary disease (COPD) has been challenging. Most previous studies have utilized individual proteins or pre-selected protein panels measured in blood samples. To identify COPD protein biomarkers by applying comprehensive mass spectrometry prot...
ORGANISM(S): Homo sapiens (Human) 
2022-01-07 | PXD024124 | Pride
Human copd chronic obstructive pulmonary disease shotgun ms/ms 
ProteomicsIceman stomach content - The 5300-year-old Helicobacter pylori genome of the Iceman
Shotgun LC-MS/MS analysis of three stomach content samples of the Iceman, a 5300-year-old European glacier mummy.
ORGANISM(S): Homo sapiens (Human) 
2018-07-20 | PXD009565 | Pride
Mummy Cid Oge Proteins Oetzi Diet Hcd Stomach content Iceman Shotgun 
ProteomicsStandard dataset of UPS1 spiked into yeast at various concentrations
A standard proteolytic digest of a human protein mixture, prepared at 1.5-fold to 3-fold protein concentration changes, and diluted into a constant background of yeast proteins. Similar to other datasets used for ground truth in quantitative studies, with the exception of being more granular, and mu...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Saccharomyces Cerevisiae (ncbitaxon:4932) 
2019-02-28 | MSV000083496 | MassIVE
ProteomicsA protein standard that emulates homology for the characterization of protein inference algorithms
A natural way to benchmark the performance of an analytical experimental setup is to use samples of known content, and see to what degree one can correctly infer the content of such a sample from the data. For shotgun proteomics, one of the inherent problems of interpreting data is that the measured...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) 
MSV000084315 | MassIVE
ProteomicsQuantification of Raloxifene Specific 471 Da Adducts in CYP3A4 and P450-Reductase
Drugs are often metabolized to reactive intermediates that form protein adducts. Adducts can inhibit critical proteins, elicit immune responses, and cause life threatening adverse drug reactions. The masses of metabolites are frequently unknown, rendering traditional mass spectrometry-based proteomi...
ORGANISM(S): Homo Sapiens Rattus Norvegicus 
2022-02-21 | PXD024932 | panorama
ProteomicsPTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline
Analysis of synthetic peptide reference datasets to demonstrate the performance of PTMProphet, a free and open-source software tool integrated into the Trans-Proteomic Pipeline, which reanalyzes identified spectra from any search engine for which pepXML output is available to provide localization co...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2025-01-10 | MSV000096828 | MassIVE
ProteomicsIPRG2015
IPRG-2015 Study -Differential Abundance Analysis in Label-Free Quantitative Proteomics. This study of LC-MS/MS data analysis focuses on data processing and statistical assessment for relative protein-level quantification in label-free proteomics.
ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932) 
2016-06-20 | MSV000079843 | MassIVE
ProteomicsDetection and Quantification of Drug-Protein Adducts in Human Liver
Protein adducts formed by drugs or their reactive metabolites are risk factors for adverse reactions, toxicity and inactivation of cytochrome P450 (CYP) enzymes. Characterization of drug-protein adducts is limited due to lack of methods capable of discovering the proteins and peptides adducted by re...
ORGANISM(S): Homo Sapiens Spodoptera Frugiperda 
2024-10-25 | PXD054246 | panorama
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