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Phosphopeptide Enrichment Coupled with Label-free Quantitative Mass Spectrometry to Investigate the Phosphoproteome in Prostate Cancer

Phosphopeptide Enrichment Coupled with Label-free Quantitative Mass Spectrometry to Investigate the Phosphoproteome in Prostate Cancer

Published on: August 2, 2018

Sample Collection Method Bias Effects in Quantitative Phosphoproteomics.

Evgeny Kanshin¹, Michael Tyers^1,2, Pierre Thibault^1,3

¹†Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada.

Journal of Proteome Research

|June 5, 2015

Summary

This summary is machine-generated.

Sample collection methods impact protein phosphorylation analysis. While many methods yield similar phosphopeptides, cold phosphate buffer unexpectedly activates signaling, potentially biasing results in phosphoproteomics studies.

Keywords:

Saccharomyces cerevisiae osmotic shock phosphoproteomics quantitative proteomics sample collection

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Published on: November 15, 2017

Area of Science:

Proteomics
Cellular signaling
Biochemistry

Background:

Advances in mass spectrometry (MS) enable large-scale phosphosite identification.
Maintaining in vivo protein phosphorylation during sample preparation is crucial.
Phosphatase inhibitors and denaturing conditions are standard for preserving phosphorylation.

Purpose of the Study:

To investigate if upstream cell collection techniques alter global protein phosphorylation.
To evaluate the impact of different sample preparation workflows on phosphorylation status.

Main Methods:

Comparison of various cell harvesting protocols (ice-cold phosphate buffer, cold ethanol, trichloroacetic acid, liquid nitrogen).
Utilized metabolic labeling and quantitative mass spectrometry.
Analysis performed on Saccharomyces cerevisiae cell cultures.

Main Results:

Highly similar phosphopeptides were identified across different harvesting methods.
Quantitative analysis revealed unexpected activation of signaling events by cold phosphate buffer.
Identified potential for systematic bias in phosphoproteomics measurements.

Conclusions:

Cell collection methods can influence phosphorylation signaling.
Cold phosphate buffer may introduce bias in phosphoproteomics and biochemical analyses.
Careful selection of sample collection protocols is essential for accurate phosphoproteomics data.