Project : PXD000807

PRIDE Assigned Tags:
Biomedical Dataset
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Summary

Title

Human oral cancer brush biopsy iTRAQ

Description

iTRAQ-based comparison of proteins derived from oral cells collected by brush biopsy. Protein abundance levels compared between oral pre-malignant cells, oral cancer cells and healthy normal cells, all collected from human patients. Two separate iTRAQ labeled biological replicate analyses were conducted.

Sample Processing Protocol

Cells were lysed, proteins digested with trypsin and iTRAQ labeled. Combined peptide mixtures were fractionated by high pH HPLC offline, and combined fractions were analyzed via LC-MS/MS on an Orbitrap Velos using HCD fragmentation.

Data Processing Protocol

Raw files were converted to mzXml using msconvert (distributed as part of ProteoWizard 1.6.1260). MS/MS spectra were searched against the Uniprot human database including scrambled sequences and common contaminant proteins (a total of 136,002 entries) using Sequest v27.0. Search parameters included a 1.6 amu (atomic mass units) precursor and 0.8 amu fragment mass tolerance, 2 missed cleavages, partial trypsin specificity, fixed modifications of carbamidomethylated cysteine, iTRAQ reagent modification at lysines and N-termini, and variable modification of methionine oxidation. Search results were filtered to 99% protein probability and 95% peptide probability in Scaffold (v3.3.1, Proteome Software), producing a false discovery rate of 1%. Proteins were quantified using customized software developed in-house call iQuant.

Contact

Tim Griffin, University of Minnesota
Timothy Jon Griffin, University of Minnesota ( lab head )

Submission Date

10/03/2014

Modification

Oxidation
Carbamidomethyl

Quantification

iTRAQ

Experiment Type

Shotgun proteomics

Assay count

2

Publication

    Yang Y, Rhodus NL, Ondrey FG, Wuertz BR, Chen X, Zhu Y, Griffin TJ. Quantitative proteomic analysis of oral brush biopsies identifies secretory leukocyte protease inhibitor as a promising, mechanism-based oral cancer biomarker. PLoS One. 2014 Apr 18;9(4):e95389. eCollection 2014 PubMed(s) : 24748380

Assay

Accession Title Protein Count Peptide Count Unique Peptide Count Spectrum Count Identified Spectrum Count
35336 no assay title provided (mzIdentML) 3126 9157 6715 8992 8992
35337 no assay title provided (mzIdentML) 4658 24603 12333 24379 24379

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