TKO6: A Peptide Standard To Assess Interference for Unit-Resolved Isobaric Labeling Platforms

Area of Science:

• Proteomics
• Analytical Chemistry
• Mass Spectrometry

Background:

• Isobaric labeling is a key quantitative mass spectrometry technique.
• Ion interference causes ratio distortion, limiting accuracy.
• Existing methods for interference assessment are limited.

Purpose of the Study:

• Introduce the TKO6 standard for measuring ion interference.
• Evaluate interference in different mass spectrometry methods.
• Improve accuracy in isobaric-tag-based protein quantification.

Main Methods:

• Developed the TKO6 standard for low mass resolution data.
• Compared interference using MS2 vs. MS3 methods.
• Assessed interference in Orbitrap Fusion and Lumos instruments.
• Compared ion-trap MS3 (IT-MS3) with Orbitrap MS3 (OT-MS3).

Main Results:

• TKO6 effectively assesses ion interference.
• Demonstrated differences in interference across acquisition methods.
• Showcased TKO6's utility in comparing IT-MS3 and OT-MS3.

Conclusions:

• The TKO6 standard is valuable for assessing quantification accuracy.
• Facilitates method development for reducing interference.
• Enhances reliability of isobaric labeling quantitative proteomics.