Protein Identification by LC-MS/MS

Trypsin-digested protein samples were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) using a Thermo-Dionex UltiMate3000 RSLCnano liquid chromatograph that was connected in line with an LTQ-Orbitrap-XL mass spectrometer equipped with a nanoelectrospray ionization source (Thermo Fisher Scientific, Waltham, MA). Data acquisition was controlled using Xcalibur software (version 2.0.7, Thermo) and data analysis was performed using Proteome Discoverer software (version 1.3, Thermo). LC-MS/MS method details have been published elsewhere [30 (link)].

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Liu T.Y., Iavarone A.T, & Doudna J.A. (2017). RNA and DNA Targeting by a Reconstituted Thermus thermophilus Type III-A CRISPR-Cas System. PLoS ONE, 12(1), e0170552.

Publication 2017

UltiMate3000 RSLCnano liquid chromatograph LTQ-Orbitrap-XL mass spectrometer Xcalibur software Proteome Discoverer software

Liquid chromatography Protein Proteome Tandem mass spectrometry Trypsin

Corresponding Organization : Lawrence Berkeley National Laboratory

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

Protein samples analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS)

control variables

Trypsin-digested protein samples
Thermo-Dionex UltiMate3000 RSLCnano liquid chromatograph
LTQ-Orbitrap-XL mass spectrometer equipped with a nanoelectrospray ionization source (Thermo Fisher Scientific, Waltham, MA)
Data acquisition controlled using Xcalibur software (version 2.0.7, Thermo)
Data analysis performed using Proteome Discoverer software (version 1.3, Thermo)

controls

No positive or negative controls are explicitly mentioned in the information provided.

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