MassIVE MSV000090663

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GNPS_High-throughput Saccharomyces cerevisiae cultivation method for credentialing-based untargeted metabolomics _SupplementaryFiles

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Description

Credentialing-based HILIC and Lipids analysis following the PAVE approach (https://doi.org/10.1021/acs.analchem.8b03132). The HILIC-based LC-MS analysis was performed with the method of Blazenovic et al., (2019)(https://doi.org/10.1021/acs.analchem.8b04698). The RP-based LC-MS lipid analysis was conducted using the method of Barupal et al., (2018)( https://doi.org/10.1038/sdata.2018.263) with adapted DDA parameters (AGC target of 1e6 and maximum injection time of 70 ms) - Raw files for the HILIC BEH for the negative ionization mode (HILIC_neg_overall_lcms) - Raw files for the HILIC BEH for the positive ionization mode (HILIC_pos_overall_lcms) - Raw files for the HILIC BEH for the negative ionization mode for the succinate quantification (HILIC_neg_succinate_lcms) - Raw files for the RP lipids analysis for the negative ionization mode ((RP_neg_overall_lcms) - Raw files for the RP lipids analysis for the positive ionization mode (RP_pos_overall_lcms) - Parsed files (.mat) for the MATLAB-based analysis with PAVE (PAVE_M) - Pre-screening with Shinyscreen for MS1/MS2 alignment and MS2 extraction for the HILIC data analysis for both ionization modes (positive and negative) and both experimental setups (SF and D48). The automatically extracted MS2 spectra are used for the annotation using MetFrag (PreeScreen_Shiny) [doi:10.25345/C5BN9X73B] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: High-throughput sample generation, liquid chromatography, metabolomics, Saccharomyces cerevisiae, stable isotope labelling, untargeted high resolution mass spectrometry

Contact

Principal Investigators:
(in alphabetical order) 		Lorenzo Favilli, University of Luxembourg, Luxembourg
Submitting User: lorenzofavilli
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GNPS content goes here (MSV000090663 [task=ba0224690964474ea64611e1f976230d])
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Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.