MassIVE MSV000087524

Partial Public

GNPS - Hela Single Cell QC kelly lab

Description

This dataset contains 3 data types: trace samples consisting of 2ng and 0.2ng aliquots of HeLa protein digest standard, and single HeLa cells. Pierce™ HeLa protein digest standard and formic acid were purchased from Thermo Fisher Scientific (Waltham, MA). Mobile phase A (0.1% formic acid in water) and mobile phase B (0.1% formic acid in acetonitrile) were respectively prepared from LC-MS grade water and acetonitrile purchased from Honeywell (Charlotte, NC). The digest standard was reconstituted to a final concentration of 200 ng/µL with 100 µL of mobile phase A to form a stock solution. For the experiments, the stock samples were further diluted to 0.2 and 2 ng/µL using the same mobile phase. HeLa cells were cultured from cells purchased from American Type Culture Culture Collection (Manassas, VA). Single HeLa cells were prepared using the nanoPOTS workflow and analyzed by manual LC injection as described previously (29797682) except that cells were isolated into nanowells using the CellenONE platform (Lyon, France) instead of by fluorescence activated cell sorting. Columns: 30-µm-i.d. fused silica capillary columns from Polymicro (Phoenix, AZ) were packed with different materials: Jupiter C18 3.0 µm, 300 Å particles and Kinetex C18 core shell particles of 1.3 µm, 100 Å µm were purchased from Phenomenex (Torrance, CA); BEH C18, 1.7 µm, 130 Å was from Waters (Milford, MA). Column lengths were adjusted to keep the pressure and the linear velocity constant for all columns. The lengths were 50, 9 and 16 cm for Jupiter, Kinetex and BEH columns respectively. Solid-phase-extraction (SPE) columns were prepared by packing Jupiter C18 particles into 100-µm-i.d. × 5-cm-long fused silica capillaries. The file names contain the sample size and lc packing material. [doi:10.25345/C5NV69] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: single cell

Contact

Principal Investigators:
(in alphabetical order)
Ryan Kelly, Brigham Young University, United States
Submitting User: hboekweg
Number of Files:
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Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
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Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
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GNPS content goes here (MSV000087524 [task=94ffc78d5b5e480bbec8b8935c8c5d6a])
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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.