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Quantitative Mass Spectrometry Proteomics

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Reconstituted samples were randomized into 8 blocks of 4 normal and 4 tumor samples. Triplicate LC–MS/MS analyses were acquired for each sample. LC separation was done on a Waters Nano Acquity UHPLC (Waters Corporation) with a Proxeon nanospray source. Mass spectra was collected on an Orbitrap Q Exactive Plus mass spectrometer (Thermo Fisher Scientific) in a data-dependent mode with one MS precursor scan followed by 15 MS/MS scans as previously described [11 (link)]. Detailed information on instrument parameters and mass spectra collection is provided in the Additional file 1: Supplemental materials and methods (1a). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [12 (link)] via the PRIDE partner repository with the dataset identifier PXD002612.

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Fahrmann J.F., Grapov D., Phinney B.S., Stroble C., DeFelice B.C., Rom W., Gandara D.R., Zhang Y., Fiehn O., Pass H, & Miyamoto S. (2016). Proteomic profiling of lung adenocarcinoma indicates heightened DNA repair, antioxidant mechanisms and identifies LASP1 as a potential negative predictor of survival. Clinical Proteomics, 13, 31.

Publication 2016

Nano Acquity UHPLC Orbitrap Q Exactive Plus mass spectrometer

Mass spectrometry Ms ms Scans Tumor

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Variable analysis

independent variables

Sample type (normal vs. tumor)

dependent variables

Proteomics data (peptide and protein abundances)

control variables

LC separation conditions
Mass spectrometry instrument parameters

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

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