MassIVE MSV000098370

Imported Reanalysis Dataset Public PXD023650

Robust micro-flow LC-MS/MS for proteome analysis – 38,000 runs and counting

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Description

Micro-flow liquid chromatography tandem mass spectrometry (µLC–MS/MS) is increasingly becoming an alternative to nano-LC–MS/MS for the analysis of proteomes. We have recently demonstrated the potential of a µLC–MS/MS system operating with a 1 mm i.d.?×?150?mm column and at a flow rate of 50?µl/min for high-throughput applications. Based on the analysis of ~38,000 samples measured on two instruments over the past two years, we show that the approach is extremely robust. Up to 1,500 analysis were performed within one month and >14,000 samples could be analyzed on a single column without loss of chromatographic performance. Samples included proteomes of cell lines, animal tissue and human body fluids, which were analyzed either with or without prior peptide fractionation or stable isotope labeling. We show that the µLC–MS/MS system is capable of measuring ~2,700 proteins from human plasma and ~5,200 proteins from human urine within one day, demonstrating its potential for in-depth as well as high-throughput clinical application. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Micro-flow lc ; Plasma ; Proteomics ; Urine ; 1.0 mm id column ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Bernhard Kuster, Chair of Proteomics and Bioanalytics, Technische Universitaet Muenchen, 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:
 
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Species

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- Dataset Reanalyses

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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.