MassIVE MSV000079571

Partial Public PXD003767

AMCA chromophore tagging and 351 nm ultraviolet photodissociation enables de novo sequencing of E. coli proteome

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Description

Demonstration of novel experimental and computational pipeline for high performance de novo peptide sequencing. E. coli whole cell lysate is carbamylated to block lysine side chains, digested with trypsin (now active only at Arg residues), and N-terminally tagged with the chromophore AMCA. Three technical replicates were analyzed using a Thermo Velos Pro dual linear ion trap mass spectrometer coupled to a Coherent 351 nm excimer laser. 351 nm ultraviolet photodissociation (UVPD) of parent peptides produces MS2 spectra dominated by the y-type ion series. We developed the software tool UVnovo for de novo sequencing of these spectra and used Proteome Discoverer SEQUEST/Percolator to generate a dataset for training and validation. UVnovo results provided here derive from a 3-fold cross validation regime. Our methods and dataset are described in the accompanying publication. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: 351 nm UVPD ; ultraviolet photodissociation ; AMCA ; de novo

Contact

Principal Investigators:
(in alphabetical order) 		Jennifer Brodbelt, Edward Marcotte
Submitting User: ahorton

Publications

Robotham SA, Horton AP, Cannon JR, Cotham VC, Marcotte EM, Brodbelt JS.
UVnovo: A De Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry.
Anal. Chem. Epub 2016 Mar 3.

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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.

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.

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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.

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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.