MassIVE MSV000095765

Imported Reanalysis Dataset Public PXD028901

MSLibrarian: Optimized predicted spectral libraries for DIA proteomics

Description

Data-independent mass spectrometry is the method of choice for deep, consistent and accurate single-shot profiling in bottom-up proteomics. While classic workflows required auxiliary DDA-MS analysis of subject samples to derive prior knowledge spectral libraries for targeted quantification from DIA-MS maps, library-free approaches based on in silico predicted libraries promise deep DIA-MS profiling with reduced experimental effort and cost. Coverage and sensitivity in such analyses, however, is limited, in part, by large library size and persistent deviations from experimental data. We present MSLibrarian, a workflow and tool to obtain optimized predicted spectral libraries by the integrated usage of spectrum-centric DIA data interpretation via the DIA-Umpire approach to inform and calibrate the in silico predicted library approach. Predicted-vs-observed comparisons enable optimization of intensity prediction parameters, calibration of retention time prediction for deviating chromatographic setups and optimization of library scope and sample representativeness. Benchmarking via a dedicated ground-truth-embedded species mixture experiment and quantitative ratio-validation confirms gains of up to 9 % on precursor and 7 % protein level at equivalent FDR control and validation criteria. MSLibrarian has been implemented as open-source R software package and, with step-by-step usage instructions, is availabe at https://github.com/MarcIsak/MSLibrarian. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Q-exactive ; Predicted spectral library ; Dia ; Hf-x ; Lfq bench

Contact

Principal Investigators:
(in alphabetical order)
Johan Malmstr�m, Infection Medicine Proteomics Lab, Division of Infection Medicine (BMC), Faculty of Medicine, Lund University, Lund, Sweden, N/A
Submitting User: ccms
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
 
FTP Download Link (click to copy):

- 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.