MassIVE MSV000087703

Partial Public

Proteomic analysis of single tears from healthy human subjects

Subscribe Comment Convert Spectra Add Reanalysis

Description

23 volunteers were recruited for this study. Tears were collected using microcapillary tubes (MCT). For each volunteer, a single tear sample was taken from one eye. For two of these volunteers, the procedure was performed in the morning (9-10 AM) and in the afternoon (5-6 PM) on the same day, once a week for 3 consecutive weeks. Proteins were purified from 5 uL of tear sample using the methanol-chloroform precipitation protocol. The lyophilized proteins were resuspended in ammonium bicarbonate 50 mM, pH 8. An in-solution trypsin digestion was performed. For each run, 1 ug of peptides was injected and each sample was injected twice. Analyses were performed by LC-MS/MS using an Orbitrap Fusion mass spectrometer coupled to an EASY-nLC 1000 nanoflow high-pressure liquid chromatography. Peptides were separated on a commercial analytical nanocolumn. MS scans were performed using the Orbitrap (OT) analyzer with a resolution of 120 000. Precursor ions were selected for higher collisional dissociation (HCD) and the collision energy was set to 30%. Dynamic exclusion was set at 45 s, with a repeat count of 1. [doi:10.25345/C5J83C] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: tear fluid ; bottom-up proteomics ; shotgun proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Erika Ponzini, University of Milano-Bicocca, Italia
Submitting User: ErikaPonzini

Publications

Erika Ponzini, Diletta Ami, Alessandro Duse, Carlo Santambrogio, Antonella De Palma, Dario Di Silvestre, Pierluigi Mauri, Fabio Pezzoli, Antonino Natalello, Silvia Tavazzi, Rita Grandori.
Single-Tear Proteomics: A Feasible Approach to Precision Medicine.
Int J Mol Sci. 2021 Oct 4;22(19):10750. doi: 10.3390/ijms221910750.

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.