Isobaric labeling enables simultaneous measurement of multiple samples, reducing analysis time and eliminating potential run-to-run variation. Here, the authors report that TMT-Integrator, now built into FragPipe, improves multiplex proteomics by speeding analysis, increasing protein and phosphosite coverage, and delivering robust results across diverse datasets and workflows.
- Hui-Yin Chang
- Yamei Deng
- Alexey I. Nesvizhskii