Shotgun Proteomics Protocol for Identification

Proteins were separated on a 2D gel and in-gel digested with trypsin (22 (link)). The resulting peptides were cleaned up using C18 OmixTips (Varian) and analyzed using an Eksigent nanoLC-2D coupled to a Thermo Orbitrap XL mass spectrometer (23 (link)). Proteins were identified from tandem mass spectra using complementary protein identification software systems, Bioworks (Thermo) and Scaffold (Proteome Software) as described by Sadygov (24 (link)).

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Buckley S., Shi W., Xu W., Frey M.R., Moats R., Pardo A., Selman M, & Warburton D. (2015). Increased alveolar soluble Annexin V promotes lung inflammation and fibrosis. The European respiratory journal, 46(5), 1417-1429.

Publication 2015

C18 OmixTips nanoLC-2D Orbitrap XL Bioworks

Peptides Protein Proteome Tandem mass spectra Trypsin

Corresponding Organization :

Other organizations : Children's Hospital of Los Angeles, Universidad Nacional Autónoma de México, Instituto Nacional de Enfermedades Respiratorias

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Variable analysis

independent variables

Separation of proteins on a 2D gel
In-gel digestion of proteins with trypsin

dependent variables

Identified proteins from tandem mass spectra

control variables

C18 OmixTips (Varian) used for peptide cleanup
Eksigent nanoLC-2D coupled to a Thermo Orbitrap XL mass spectrometer used for analysis
Bioworks (Thermo) and Scaffold (Proteome Software) used for protein identification

controls

No positive or negative controls were explicitly mentioned in the input protocol.

Annotations

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