Home » Abstracts » Other » Six years of optimizations of automated sample preparation protocols for routine use in proteomics

Six years of optimizations of automated sample preparation protocols for routine use in proteomics

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Abstract #240 Posted on28 March 202525 April 2025 25 April 2025 11h12

Author(s)

Valériane Gaxotte (Presenting Author) | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France
Magali Rompais | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France
Jeewan Babu Riijal | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France
Hugo Gizardin-Fredon | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France
Charlotte Brun | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France
Marie Gebelin | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France
Chloe Moritz | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France
Sarahi Jaramillo ortiz | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France
Noelia-milagros De Lama Valderrama | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France
Delphine Rolland | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France
fabrice bertile | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France
Laurence Ehret-Sabatier | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France
Sarah Cianferani | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France
Christine Carapito | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France
Christine Schaeffer-Reiss | LSMBO-ProFI-IPHC-CNRS | 25, rue Becquerel, 67087, Strasbourg, France

Abstract

The instrumental revolution in mass spectrometry-based proteomics has allowed for higher throughput with increased sensitivity and reduced amounts of starting material requirements. Sample preparation automation arose as a critical step of the proteomics workflow in order to gain sample homogeneity, repeatability, accuracy and preparation time. Here, we present the optimized protocols on a Bravo AssayMap from Agilent, installed in our lab in 2019, for a plethora of proteomics applications: routine desalting, PTMs enrichment (phosphorylation, glycation, chemical probe…), host cell protein enrichment, crosslinking, or protein purifications.
The protocols were adapted for a large variety of sample types and experimental constraints linked to the multiplicity of projects handled in the lab. This poster will review conducted optimizations to improve the performances and robustness of the protocols and provide tips and tricks accumulated through our collective experiences.
Today, the instrument is used by most of the lab members with a growing frequency for many different protocols: peptide clean-up, auto-SP3, enrichment, peptide fractionation, in solution digestion, affinity purification, and immobilization.
As a general conclusion, the system has proven a fairly good robustness over the years, provided that users get a good training and strict user-guidance is maintained. Initiating exchanges on common automation practices is the aim of this poster.

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The instrumental revolution in mass spectrometry-based proteomics has allowed for higher throughput with increased sensitivity and reduced amounts of starting material requirements.  Sample preparation automation arose as a critical step of the proteomics workflow in order to gain sample homogeneity, repeatability, accuracy and preparation time. Here, we present the optimized protocols on a Bravo AssayMap from Agilent, installed in our lab in 2019, for a plethora of proteomics applications: routine desalting, PTMs enrichment (phosphorylation, glycation, chemical probe…), host cell protein enrichment, crosslinking, or protein purifications. 
The protocols were adapted for a large variety of sample types and experimental constraints linked to the multiplicity of projects handled in the lab. This poster will review conducted optimizations to improve the performances and robustness of the protocols and provide tips and tricks accumulated through our collective experiences.  
Today, the instrument is used by most of the lab members with a growing frequency for many different protocols: peptide clean-up, auto-SP3, enrichment, peptide fractionation, in solution digestion, affinity purification, and immobilization. 
As a general conclusion, the system has proven a fairly good robustness over the years, provided that users get a good training and strict user-guidance is maintained. Initiating exchanges on common automation practices is the aim of this poster.

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