MassIVE MSV000097090

Partial Public

Proteoform identification using multiplexed top-down mass spectra

Subscribe Comment Reanalyze Spectra Add Reanalysis

Description

A total of 300 ng of E. coli protein was analyzed using a Thermo Scientific (Waltham, MA, USA) Ultimate 3000 reverse-phase liquid chromatography (RPLC) system equipped with a C2 column (100-micrometer i.d., 60 cm length, CoAnn, Richland, WA, USA) and coupled to a Thermo Orbitrap Lumos mass spectrometer (Waltham, MA, USA). Mobile phase A was water with 0.1% formic acid (FA). Mobile phase B was 60% acetonitrile (ACN), 15% isopropanol (IPA) and 25% water with 0.1% FA. A 98-min gradient (0-5 min 5%, 5-7 min for 5% to 35%, 7-10 min for 35% to 50%, 10-97 min for 50% to 80%, 97-98 min for 80% to 99%) was applied for proteoform separation with a flow rate of 400 nL/min. MS1 scans were collected at a resolution of 240,000 (at 200 m/z) with 4 microscans, a maximum injection time of 200 ms, and a scan range of 720-1200 m/z. The top 6 precursors in each MS1 scan were selected for Higher-energy C-trap dissociation (HCD) MS/MS analyses with following settings: the precursor isolation window was 3 m/z, the normalized collision energy was 30%; the Automated Gain Control (AGC) target was 106, and the maximum injection time was 500 ms; the microscan number was 1; the resolution was 60,000 (at 200 m/z); and the scan range was 400-2000 m/z. [doi:10.25345/C5P26QG2M] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: top down proteomics ; TopPIC ; TopMPI ; TDP ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Xiaowen Liu, Tulane University, United States
Submitting User: zwang64
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:
 
Browse Dataset Files
 
FTP Download Link (click to copy):

Species

Instrument

Modifications

- Dataset Reanalyses

+ Dataset History

Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

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.