MassIVE MSV000089291

Partial Public

Proteomic analysis of lung cancer types

Description

Formalin fixed and paraffin embedded (FFPE) AC, SqCC, LCC, SCLC (n=10, 9, 10, 9, respectively) and tumor adjacent normal tissue sections (n=8, 8, 8, 9, respectively) were analyzed. Samples were analyzed using a Maxis II QTOF instrument equipped with a CaptiveSpray nanoBooster ion source coupled to a Dionex UltiMate 3000 RSLCnano system (Bruker Daltonics GmbH, Bremen, Germany). Peptides were separated on an Acquity M Class BEH130 C18 analytical column (1.7 um, 75 um x 250 mmu) using gradient elution (isocratic hold at 4% for 11 min, then elevating B solvent content to 25% in 75 min, and to 40% in 15 min) following trapping on an Acclaim PepMap100 C18 (5 um, 100 um x 20 mmu) trap column. Solvent A consisted of 0.1% FA in water, Solvent B was 0.1% FA in ACN, and the sample loading buffer was 0.1% TFA + 0.01% HFBA in water. For MS analysis, DDA measurements were performed. The cycle time was set at 2.5 s, with a dynamic MS/MS exclusion of the same precursor ion for 2 min, or if its intensity is at least 3 times larger than previously. Preferred charge states were set between + 2 and + 5. MS spectra were acquired at 3 Hz in the 150 to 2200 m/z range, while MS/MS spectra were at 4 or 16 Hz depending on the intensity of the precursor. Internal calibration was performed by infusing sodium formate and raw data were recalibrated using the Compass DataAnalysis software 4.3. [doi:10.25345/C5FB4WQ6K] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: lung cancer ; lung tissue ; cancer ; proteomics ; mass spectrometry ; HPLC-MS

Contact

Principal Investigators:
(in alphabetical order)
Lilla Turiak, MS Proteomics Research Group, Research Centre for Natural Sciences, Eotvos Lorand Research Network, Hungary
Submitting User: rozmarakiraly
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Experimental Design
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Identification Results
    Proteins (Human, Remapped):
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Quantification Results
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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

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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.

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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.

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