MassIVE MSV000092199

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Parallel gradients in comprehensive two_dimensional liquid chromatography_mass spectrometry for complex protein digest analysis

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Description

Here we describe the development of a parallel gradient method for protein digest analysis, investigating parameters such as gradient program, flow rate and modulation time. High 2D surface coverage and peak capacity were obtained (peak capacity of 679 in 60 minutes). Moreover, the use of parallel gradients is favorable to favor LCxLC HRMS coupling, removing the need for postcolumn splitting preHRMS with allowing separation at reduced flow rates in the second dimension (0.7 mL/ min), removing the need for post-column splitting pre-HRMS. The analysis of human cell culture lysate digest by parallel RPLCxRPLC MS/MS resulted in identifying 8959 peptides and 1984 proteins within 1hr run. This was a gain of 149% in the number of peptides identified compared to 1DLC method. [doi:10.25345/C58S4K03X] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: 2DLC ; Parallel gradients ; Peptide analysis

Contact

Principal Investigators:
(in alphabetical order) 		Andrea Gargano, University of Amsterdam, The Netherlands
Submitting User: agargan1
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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.

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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.

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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.

"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.