Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics | IonOpticks

Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics

Dijana

6 November 2023
Publications / By

A recent study using IonOpticks Aurora Series Columns compares the performance of widely used software and workflows for data-independent acquisition (DIA) proteomics and phosphoproteomics. The researchers generated a reference dataset for benchmarking and evaluated four popular software suites using various metrics. The results indicated that different software suites exhibit distinct strengths and weaknesses depending on the type of experiment, and there is no single “best” software for all DIA proteomics and phosphoproteomics applications. The researchers also provided recommendations for selecting software based on experimental needs and outlined the importance of transparency and reproducibility in DIA proteomics and phosphoproteomics research. Overall, this study provides valuable insights for researchers seeking to optimize their DIA proteomics and phosphoproteomics analyses. https://www.nature.com/articles/s41467-022-35740-1

The effectiveness of the IonOpticks Aurora 25cm column in establishing a robust and dependable method for proteomic analysis is underscored in this research.

Journal Article – Jan 2023  – Nature Communications

Authors 

R. Lou; Y. Cao; S. Li; X. Lang; Y. Li; Y. Zhang; W. Shui

Title

Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics

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Byoung-Kyu Cho, Team Lead, Proteomics
Byoung-Kyu Cho, Team Lead, Proteomics

Washington University in St. Louis, School of Medicine

With over a decade of experience in proteomics research, I can confidently say that the IonOpticks column is the superior choice. Its exceptional analytical performance in terms of sensitivity and reproducibility has allowed me to maximize protein identification in any biological sample. Additionally, the column is robust and can withstand hundreds of runs without significant loss of performance. The customer service team is outstanding, always quick to respond to any questions or concerns. I highly recommend IonOpticks columns to any researcher seeking high-quality mass spectrometry data.

Daniel Itzhak, Director, Mass Spectrometry
Daniel Itzhak, Director, Mass Spectrometry

Altos Labs

I have been using IonOpticks columns for 4 years, their performance is phenomenal, superior to any column I could pack myself, and they last at least 5 times as long. Switching to IonOpticks has saved me a huge amount of time, I simply do not have to stress about chromatography any more. The team are also responsive, and it is clear that customer satisfaction is important to them. Keep up the great work folks!

Neal Gould, Principal Scientist
Neal Gould, Principal Scientist

Tegmine Therapeutics

The Aurora columns are fantastic. Not only do they perform better than other columns on the market but they're durable and the single nano connection makes setup easy and simplifies troubleshooting. I use them for all my routine peptide and PTM applications.

Emmanuelle Lezan, Principal Associate
Emmanuelle Lezan, Principal Associate

F. Hoffmann-La Roche, Switzerland

We switched all our instruments with a 15 or 25cm aurora column for 1 year. Their performance, spray stability and robustness are really appreciated. We have really good results in label-free and DIA workflow compared to other columns used.

Assoc. Prof. Nikolai Slavov
Assoc. Prof. Nikolai Slavov

Northeastern University

We obtained better results with IonOpticks...

 

We were able to leverage the very high accuracy of retention times as an additional feature to increase confidence in correct peptide identifications and to reduce confidence in incorrect ones.

Akinori Endo, PhD
Akinori Endo, PhD

Laboratory of Protein Metabolism
Tokyo Metropolitan Institute of Medical Science
Tokyo, Japan

We are very pleased with the performance of the Aurora column that can be applied to most proteomics studies. They allow us to acquire MS data with higher quality and especially improved in-depth proteomics output.

Dr. Alex von Kriegsheim
Dr. Alex von Kriegsheim

Edinburgh Cancer Research UK Centre
Institute of Genetics and Molecular Medicine
University of Edinburgh

We have switched all our instruments from in-house packed 35cm emitters to Aurora columns. Their performance is equal or superior to our in-house packed columns, their spray-stability and durability is exceptional, they are fool-proof to install and last hundreds of runs.

Martin R. Larsen, PhD
Martin R. Larsen, PhD

Protein Research Group, University of Southern Denmark
Odense, Denmark

We have recently started to use the Aurora columns and they significantly outperform any other columns that we have ever used for nano-LC-MSMS, by providing much higher peptide coverage in proteomics and phosphoprotemics.

Dr. Ignasi Forne
Dr. Ignasi Forne

Ludwig-Maximilians-Universität
Planegg-Martinsried, Germany

I am very happy with the robustness and performance of IonOpticks Aurora columns. They have significantly improved the results of my label-free quantitative workflows.