Multi-laboratory analysis of the variability of shipped samples for proteomics following non-cooled international transport

Pascal Steffen; Christoph Krisp; Wang Yi; Pengyuan Yang; Mark P Molloy; Hartmut Schlüter

doi:10.1016/j.ab.2018.02.026

Multi-laboratory analysis of the variability of shipped samples for proteomics following non-cooled international transport

Anal Biochem. 2018 May 1:548:60-65. doi: 10.1016/j.ab.2018.02.026. Epub 2018 Feb 25.

Authors

Pascal Steffen¹, Christoph Krisp², Wang Yi³, Pengyuan Yang⁴, Mark P Molloy⁵, Hartmut Schlüter⁶

Affiliations

¹ Mass Spectrometric Proteomics Group, Department of Clinical Chemistry and Central Laboratories, University Medical Center Hamburg-Eppendorf (UKE), Martinistrasse 52, Building N27, Room 00.008, Hamburg, 20246, Germany; Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility (APAF), Macquarie University, E8C310, Research Park Drive, Sydney, NSW, 2109, Australia. Electronic address: p.steffen@uke.de.
² Mass Spectrometric Proteomics Group, Department of Clinical Chemistry and Central Laboratories, University Medical Center Hamburg-Eppendorf (UKE), Martinistrasse 52, Building N27, Room 00.008, Hamburg, 20246, Germany; Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility (APAF), Macquarie University, E8C310, Research Park Drive, Sydney, NSW, 2109, Australia. Electronic address: c.krisp@uke.de.
³ Department of Chemistry and Institute for Biomedical Sciences, Fudan University, Shanghai, China. Electronic address: yiwang@fudan.edu.cn.
⁴ Department of Chemistry and Institute for Biomedical Sciences, Fudan University, Shanghai, China. Electronic address: pyyang@fudan.edu.cn.
⁵ Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility (APAF), Macquarie University, E8C310, Research Park Drive, Sydney, NSW, 2109, Australia. Electronic address: mark.molloy@mq.edu.au.
⁶ Mass Spectrometric Proteomics Group, Department of Clinical Chemistry and Central Laboratories, University Medical Center Hamburg-Eppendorf (UKE), Martinistrasse 52, Building N27, Room 00.008, Hamburg, 20246, Germany. Electronic address: hschluet@uke.de.

PMID: 29486204
DOI: 10.1016/j.ab.2018.02.026

Abstract

Transporting biological samples such as cells or tissues is complicated by the need to maintain integrity and minimise modification and degradation, but this is economically costly as the samples must be shipped in a frozen state. This multi-laboratory study investigated sample variability introduced by non-cooled transport of dried peptide samples for proteomic analysis using mass spectrometry. Human cancer cell tryptic lysates were proteolysed and dried in Australia and shipped by air to Europe and China. Samples were measured using label free mass spectrometry on similar LC-MS systems at all three sites. Preparation and analysis of the specimens in this manner resulted in only minor differences in protein identification and showed high quantitative reproducibility amongst the participating laboratories. We examined any impact on peptide chemical modification and report no discrepancies compared to the starting, non-shipped sample. We conclude that transport of non-cooled, dried peptides has negligible effect on sample integrity for downstream LC-MS analysis and therefore represents a cost-effective option to facilitate international proteomic collaborations. Data is available via ProteomeXchange with identifier PXD008160.

Keywords: LC-MS; Multi-laboratory; Peptides; Proteomics; Stability.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Line, Tumor
Chromatography, Liquid
Humans
Mass Spectrometry*
Neoplasm Proteins* / chemistry
Neoplasm Proteins* / metabolism
Neoplasms* / chemistry
Neoplasms* / metabolism
Peptides* / chemistry
Peptides* / metabolism
Proteomics / methods*
Specimen Handling / methods*

Substances

Neoplasm Proteins
Peptides