MassIVE MSV000081545

Imported Reanalysis Dataset Public PXD001464

Multiphasic chip performance characterization using human thyroid cancer cell line SW1736 and human plasma

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Description

Development of an online peptide fractionation system comprising a multiphasic LC chip that integrates reversed phase and strong cation exchange chromatography upstream of the MS based on the multi-dimensional protein identification technology (mudPIT). Chips were assessed in terms of chromatographic as well as protein and peptide identification reproducibility using five-step fractionation of 0, 2, 50, 500 and 1500 mM ammonium acetate. Further, a comparison of multiphase LC chip protein and peptide identification versus conventional reversed phase LC-MSMS was performed. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Chip LC-MSMS ; Multiphasic LC chip separation ; thyroid cancer cell line ; human plasma

Contact

Principal Investigators:
(in alphabetical order) 		Assoc Prof Mark P Molloy, Macquarie University Australian Proteome Analysis Facility (APAF) Sydney, Australia, N/A
Submitting User: ccms

Publications

Krisp C, Yang H, van Soest R, Molloy MP.
Online Peptide fractionation using a multiphasic microfluidic liquid chromatography chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics.
Mol. Cell Proteomics. 2015 Jun;14(6):1708-19. Epub 2015 Apr 7.

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Experimental Design
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Identification Results
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Quantification Results
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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.