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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
ProteomicsA comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS
A comprehensive and high-quality E. coli spectral assay library for 56,182 proteotypic peptides mapped to 4,014 (91.5%) of the 4,389 annotated proteins using one- and two-dimensional fractionated samples, and ion mobility separation.
ORGANISM(S): Escherichia coli 
2020-10-19 | PXD020761 | Pride
Dia-ms Spectral assay library E. coli 
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
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 (Human) Saccharomyces cerevisiae (Baker's yeast) 
2018-09-24 | PXD006447 | Pride
Dilution series Yeast Standard Ups1 
ProteomicsProteomic analysis of Plasmodium yoelii salivary gland sprozoites
Proteomic analysis of Plasmodium yoelii salivary gland sprozoites
ORGANISM(S): Plasmodium yoelii yoelii 17XNL 
2019-10-02 | PXD009727 | Pride
Plasmodium yoelii Salivary gland sprozoite 
ProteomicsProteomic analysis of Plasmodium falciparum salivary gland sporozoites
Proteomic analysis of Plasmodium falciparum salivary gland sporozoites
ORGANISM(S): Plasmodium falciparum NF54 
2019-10-02 | PXD009726 | Pride
Plasmodium falciparum Malaria Salivary gland sporozoite 
ProteomicsVacuum insulated probe heated electrospray ionization source (VIP-HESI) significantly enhances micro flow rate chromatography signals in the Bruker timsTOF mass spectrometer.
Nano-flow chromatography-tandem mass spectrometer (nLC-MS/MS) is a popular choice in proteome research as it provided high-sensitivity analysis with minimal sample usage, but its quantitative proteomics applications become restricted by low analytical throughput, and low robustness. To circumvent th...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2023-05-24 | PXD040497 | Pride
Slice-pasef Electrospray ionization (esi) Dia-pasef Micro-flow rate chromatography Vacuum insulated probe heated electrospray ionization source (vip-hesi) Captive spray (cs) 
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
ProteomicsDDA data of Felis Catus immortalized cells, tissues and plasma
We report a mass spectrometry-based proteomics approach to advance the study of the feline proteome. We analyzed immortalized feline cells, various tissues and plasma using data-dependent acquisition (DDA) on a Q Exactive HF mass spectrometer to develop a Felis Catus PeptideAtlas from 157 acquired r...
ORGANISM(S): Felis catus (Cat) (Felis silvestris catus) 
2026-07-07 | PXD075481 | Pride
Feline cell lines Tissues Plasma Peptideatlas Data-dependent acquisition Felis catus  cat proteome 
ProteomicsImproved analysis of crosslinking mass spectrometry data with Kojak 2.0, advanced by integration into the Trans-Proteomic Pipeline
Fragmentation ion spectral analysis of chemically crosslinked proteins is an established technology in the proteomics research repertoire for determining protein interactions, spatial orientation, and structure. Here we present Kojak version 2.0, a major update to the original Kojak algorithm, which...
ORGANISM(S): Bos taurus (Bovine) Saccharomyces cerevisiae (Baker's yeast) 
2023-01-18 | PXD037492 | Pride
Kojak Crosslinking mass spectrometry Proteomics Software tools Protein interaction Peptideprophet Xl-ms Trans-proteomic pipeline Computational proteomics Iprophet 
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