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MetabolomicsA combined direct infusion/reversed phase chromatography – high resolution mass spectrometry workflow for accurate absolute lipid quantification with 13C- internal standards
We propose a fully automated novel workflow for lipidomics based on flow injection, followed by liquid chromatography-high-resolution mass spectrometry (FI/LC-HRMS). The workflow combined in-depth characterization of the lipidome achieved via reversed-phase LC-HRMS with absolute quantification by us...
2021-07-01 | MTBLS1876 | MetaboLights
ProteomicsTMTPro Complementary Ion Quantification Increase Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 level
The ability of the TMTPro isobaric labeling reagents to form complementary ions for accurate multiplexed proteomics at the MS2 level was investigated. Human and yeast peptides were labeled in distinct ratios to analyze the effect of interference on the quantification accuracy. A method, TMTProC, was...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2021-05-11 | PXD021661 | Pride
Complementary ion quantification Interference-free quantification Multiplexing Tmtpro 
ProteomicsComparative Evaluation of MaxQuant and Proteome Discoverer MS1-based Protein Quantification Tools
MS1-based label-free quantification can compare precursor ion peaks across runs, allowing reproducible protein measurements. Among bioinformatic platforms enabling MS1-based quantification, MaxQuant (MQ) is one of the most used, while Proteome Discoverer (PD) has recently introduced the Minora tool....
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2021-05-31 | PXD022169 | Pride
Dynamic range Proteomics Mass spectrometry Specificity Sensitivity Accuracy Precision Label-free quantification Differential analysis 
ProteomicsCombining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition
In data independent acquisition, consistent, comprehensive MS1 and MS2 can be recorded. This enables statistical comparison based on the two quantitative levels.
ORGANISM(S): Arabidopsis Thaliana (ncbitaxon:3702) Escherichia Coli (ncbitaxon:562) Saccharomyces Cerevisiae (ncbitaxon:4932) Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) Caenorhabditis Elegans (ncbitaxon:6239) 
2020-01-30 | MSV000084864 | MassIVE
MetabolomicsMetaboKit: a comprehensive data extraction tool for untargeted metabolomics (Standard mixture assay)

We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis. In data dependent acquisition (DDA) analysis, MetaboKit constructs a customized spectral library with compound identit...

2021-11-05 | MTBLS1311 | MetaboLights
MetabolomicsMetaboKit: a comprehensive data extraction tool for untargeted metabolomics (Mouse liver assays)

We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis. In data dependent acquisition (DDA) analysis, MetaboKit constructs a customized spectral library with compound identit...

2021-11-02 | MTBLS1266 | MetaboLights
ProteomicsMulti-parameter optimization of two common proteomics quantification methods for quantifying low-abundance proteins
To improve the sensitivity and accuracy of label-free quantification and tandem mass tags (TMT) labeling in quantifying low-abundance proteins, multi-parameter optimization was carried out using a complex 2-proteome artificial sample mixture for a series of steps from sample preparation to data anal...
ORGANISM(S): Homo Sapiens Mus Musculus 
2018-11-02 | PXD011574 |
ProteomicsMS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions
Quantitative analysis of discovery-based proteomic workflows now relies on high-throughput large-scale methods for identification and quantification of proteins and post-translational modifications. Advancements in label-free quantitative techniques, using either data-dependent or data-independent m...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2015-04-01 | MSV000079092 | MassIVE
ProteomicsAn ultra-high-resolution IonStar strategy enhancing accuracy and precision of MS1-based proteomics and an extensive comparison with state-of-the-art SWATH-MS in large-cohort quantification
Quantitative proteomics in large cohorts is highly valuable for biomedical/pharmaceutical investigations but often suffers from suboptimal reliability, accuracy, and reproducibility. Here we describe a new ultra-high-resolution (UHR) IonStar method achieving precise/reproducible protein measurement ...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2021-06-24 | PXD017915 | Pride
Ultrahigh resolution ionstar 240k quantification 
MetabolomicsCustomized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow
Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions t...
2018-03-26 | MTBLS417 | MetaboLights
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