MassIVE MSV000086614

Complete Public PXD023205

Experimental validation of a central carbon metabolic model in Aspergillus niger to enable metabolic engineering of a fungal cell factory

Subscribe Comment Convert Spectra Reanalyze Spectra Compare Results Add Reanalysis

Description

The influence of selected pentose catabolic pathway (PCP) deletion strains on growth of plant biomass and re-routing of sugar catabolism was addressed to gain a better understanding of the flexibility of the fungus Aspergillus niger in using plant biomass-derived monomers. The transcriptome, metabolome and proteome response of three PCP mutant strains grown on wheat bran (WB) and sugar beet pulp (SBP) were evaluated. Proteomics samples were digested with trypsin then analyzed by LC-MS/MS with fractionation. Metabolomics samples were derivitized using a modified Fiehn protocol and analyzed by GC-MS with FAME added for retention alignment. Proteomics data was searched with MS-GF+ using PNNL's DMS Processing pipeline. [doi:10.25345/C5B49D] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: lignocellulosic substrates ; pentose catabolic pathway ; D-galacturonic acid catabolic pathway ; L-rhamnose catabolic pathway, ; wheat bran ; sugar beet pulp ; CAZymes

Contact

Principal Investigators:
(in alphabetical order) 		Ronald de Vries, Westerdijk Fungal Biodiversity Institute, Netherlands
Submitting User: alchemistmatt

Publications

Chroumpi T, Peng M, Markillie LM, Mitchell HD, Nicora CD, Hutchinson CM, Paurus V, Tolic N, Clendinen CS, Orr G, Baker SE, Mäkelä MR, de Vries RP.
Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates.
Front Bioeng Biotechnol. Epub 2021 Mar 8.

Number of Files:
Total Size:
Spectra:
Subscribers:
 
Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
Browse Dataset Files Browse Results
 
FTP Download Link (click to copy):

Species

Instrument

Modifications

- Dataset Reanalyses

+ Dataset History

Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
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.

"N/A" means no results of this type were submitted.
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.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
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.

"N/A" means no results of this type were submitted.
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.