Quantitative Proteomics Using UHPLC-MS/MS

Tryptic digests were analyzed on a 6495C triple quadrupole mass spectrometer (Agilent) coupled to a 1290 Infinity II UHPLC system (Agilent). Prior to MS analysis, samples were chromatographically separated on an InfinityLab Poroshell 120 EC‐C18 column (2.1 × 50 mm, 1.9 μm, Agilent) heated to 45°C with a flow rate of 800 μl/min. The 6495C mass spectrometer was controlled by MassHunter Workstation software (LC–MS/MS Data Acquisition for 6,400 series Triple Quadrupole, Version 10.1 (Agilent)) and was operated in positive electrospray ionization mode. Samples were analyzed in dynamic multiple reaction monitoring (MRM) mode with both quadrupoles operating at unit resolution (Wang et al, 2022a (link)).

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Wang Z., Tober‐Lau P., Farztdinov V., Lemke O., Schwecke T., Steinbrecher S., Muenzner J., Kriedemann H., Sander L.E., Hartl J., Mülleder M., Ralser M, & Kurth F. (2022). The human host response to monkeypox infection: a proteomic case series study. EMBO Molecular Medicine, 14(11), e16643.

Publication 2022

6495C triple quadrupole mass spectrometer 1290 Infinity II UHPLC system InfinityLab Poroshell 120 EC‐C18 column

Ms ms Tryptic

Corresponding Organization :

Other organizations : Charité - Universitätsmedizin Berlin, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Wellcome Centre for Human Genetics, University of Oxford

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Variable analysis

independent variables

Chromatographic separation on an InfinityLab Poroshell 120 EC‐C18 column (2.1 × 50 mm, 1.9 μm, Agilent)

dependent variables

Tryptic digests analyzed on a 6495C triple quadrupole mass spectrometer (Agilent)

control variables

Column temperature of 45°C
Flow rate of 800 μl/min
Positive electrospray ionization mode
Dynamic multiple reaction monitoring (MRM) mode
Both quadrupoles operating at unit resolution

controls

No positive or negative controls were explicitly mentioned.

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