# Proteome-Wide Multipoint Internal Calibration Curves for Evaluating Peptide-Level Linearity in Relative Quantitative Proteomics

## TL;DR

This paper introduces a new method using TMT to create internal calibration curves for all peptides in a proteome, improving accuracy in relative quantification.

## Contribution

A novel TMT-based multipoint internal calibration strategy for proteome-wide peptide linearity assessment in a single experiment.

## Key findings

- The new strategy enables internal calibration curves for all identified peptides in a proteome.
- Application to human ovarian cancer cells revealed significant proteome changes after cisplatin treatment.

## Abstract

Mass spectrometry (MS)-based proteomics is known for
its high accuracy
in quantifying peptides and proteins using various calibration strategies
including internal and external calibration curves. While external
multipoint calibration curves are created from serial dilutions, they
often fail to account for sample-specific matrix effects. In contrast,
internal calibration curves account for the sample matrix but face
scalability and cost challenges for whole proteome analyses. In this
manuscript, we present a novel TMT-based multipoint internal calibration
curve strategy, which enables the generation of internal calibration
curves for all peptides identified within a proteome in a single experiment
to assess their linearity prior relative quantification. We applied
this strategy to human ovarian cancer cells to evaluate the linear
quantitative responses of all of the identified peptides and reveal
the significant proteome changes associated with cisplatin treatment.