Quantitative Proteomics by LC-MS/MS

LC-MS/MS analysis was performed using a Dionex Ultimate 3000 nano-ultra high-pressure reverse-phase chromatography coupled on-line to a Q Exactive HF mass spectrometer (Thermo Scientific) as described previously (Fye et al., 2018 (link)). In brief, samples were separated on an EASY-Spray PepMap RSLC C18 column (500 mm × 75 μm, 2 μm particle size, Thermo Scientific) over a 60 min gradient of 2–35% acetonitrile in 5% dimethyl sulfoxide (DMSO), 0.1% formic acid at 250 nL/min. MS1 scans were acquired at a resolution of 60,000 at 200 m/z and the top 12 most abundant precursor ions were selected for high collision dissociation (HCD) fragmentation.

Free full text: Click here

Pinto-Fernández A., Davis S., Schofield A.B., Scott H.C., Zhang P., Salah E., Mathea S., Charles P.D., Damianou A., Bond G., Fischer R, & Kessler B.M. (2019). Comprehensive Landscape of Active Deubiquitinating Enzymes Profiled by Advanced Chemoproteomics. Frontiers in Chemistry, 7, 592.

Publication 2019

Q Exactive HF mass spectrometer EASY-Spray PepMap RSLC C18 column

Acetonitrile Dimethyl sulfoxide Formic acid Ions Ms ms Pressure Reverse phase chromatography Scans

Corresponding Organization : University of Oxford

Other organizations : Canterbury Christ Church University, Ludwig Cancer Research, Goethe University Frankfurt

Top 5 similar protocols

Protocol cited in 1 other protocol

Variable analysis

independent variables

Gradient of 2–35% acetonitrile in 5% dimethyl sulfoxide (DMSO), 0.1% formic acid at 250 nL/min

dependent variables

MS1 scans acquired at a resolution of 60,000 at 200 m/z
Top 12 most abundant precursor ions selected for high collision dissociation (HCD) fragmentation

control variables

EASY-Spray PepMap RSLC C18 column (500 mm × 75 μm, 2 μm particle size, Thermo Scientific)

controls

No specific positive or negative controls were mentioned.

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!