This Application Note demonstrates the Agilent Nanoflow Proteomics Solution system1) as a powerful tool for analysis of proteomics samples. Using the approach of cation exchange, sample enrichment, reversed phase chromatography and nanospray ion trap mass spectrometry with subsequent database search, all of ten proteins were identified from a tryptic digestion model mixture and hundreds of proteins from a complex E. coli cell lysate.
This document serves as an application note demonstrating the capabilities of the Agilent Nanoflow Proteomics Solution system. It details a workflow for analyzing complex proteomic samples by combining two-dimensional liquid chromatography (2D LC) with nanoelectrospray ion trap mass spectrometry (MS/MS). The methodology utilizes strong cation exchange chromatography for sample enrichment followed by reversed-phase chromatography.
The note presents results from the analysis of a tryptic digestion model mixture containing ten proteins and a complex E. coli cell lysate. It describes the specific equipment used, including the Agilent 1100 Series nanoflow pump, autosampler, column compartment, and LC/MSD Trap SL, along with the software employed for data acquisition and database searching.
| System Name | Agilent Nanoflow Proteomics Solution |
|---|---|
| Pump Type | Agilent 1100 Series nanoflow pump |
| Autosampler | Agilent 1100 Series micro well-plate autosampler |
| Column Compartment | Agilent 1100 Series thermo-statted column compartment |
| MS Source | nanoflow electrospray ion source |
| Software | Agilent ChemStation A09.02 and ion trap software 4.1 |
| Database Search Software | Mascot software |
To demonstrate the Agilent Nanoflow Proteomics Solution system as a tool for analyzing proteomics samples.
The method combines strong cation exchange chromatography with reversed-phase LC separation.