MassIVE MSV000092055

Partial Public PXD042548

Cysteine Counting via Isotopic Chemical Labeling for Intact Mass Proteoform Identifications in Tissue

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Description

This data set contains raw files from the following samples: 1) a simple standard mixture of proteins used for optimization of labeling conditions and 2) human proteoforms extracted from a biopsied prostate tumor sample. Standard proteins are labeled with the natural-isotopic version of a cysteine-specific chemical labeling reagent, dimethyl-leucine hydrazide (DLH) (Modification mass: 213.1479 Da, Modification formula: C10 H19 O2 N3). 3 technical replicates of 3 replicate labeling experiments performed at the optimized labeling conditions are provided. Extracted prostate tumor proteoforms were split into two portions and 1 was labeled with the NeuCode-light DLH isotopologue (Modification mass: 222.15896 Da), and the other was labeled with the NeuCode-heavy DLH isotopologue (222.20422). After labeling, these samples were combined in a 2:1 ratio (NeuCode heavy:NeuCode light). The combined proteoforms were separated into 8 size-based fractions using PEPPI fractionation. The following intact-mass (i.e. LC-MS, no precursor fragmentation) files were collected: Fractions 1-4 were analyzed at MS1 resolutions of 240,000 and 500,000. Fractions 5 and 6 were analyzed at MS1 resolutions of 120,000, 240,000, and 500,000. Fractions 7 and 8 were analyzed at MS1 resolutions of 120,000 and 240,000. This produced 18 intact-mass LC-MS raw files. Each fraction was also analyzed by Top-down mass spectrometry (LC-MS/MS), producing 8 LC-MS/MS raw files. Also included are: 1) a database containing the proteins in the mixture on which labeling optimization was performed 2) a protein-pruned GPTMD database derived from previous BU analysis of prostate tumors used to search the TD and NeuCode intact-mass data 3) the proteoform atlas produced from the collected TD data and used to search the NeuCode intact-mass data. [doi:10.25345/C5RN30J3N] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: NeuCode ; Chemical Labeling

Contact

Principal Investigators:
(in alphabetical order) 		Lloyd M. Smith, University of Wisconsin - Madison, USA
Submitting User: jgpavek1217
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Identification 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.

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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.