Minimal sample requirement for highly multiplexed protein quantification in cell lines and tissues by PCT-SWATH mass spectrometry
Shiying Shao, Tiannan Guo, Chiek Ching Koh, Silke Gillessen, Markus Joerger, Wolfram Jochum & Ruedi Aebersold
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abstract
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The amount of sample available for clinical and biological proteomic
research is often limited and thus significantly restricts clinical
and translational research. Recently, we have integrated pressure
cycling technology (PCT) assisted sample preparation and SWATH-MS to
perform reproducible proteomic quantification of biopsy-level tissue
samples. Here, we further evaluated the minimal sample requirement
of the PCT-SWATH method using various types of samples, including
cultured cells (HeLa, K562, and U251, 500 000 to 50 000 cells) and
tissue samples (mouse liver, heart, brain, and human kidney, 3-0.2
mg). The data show that as few as 50 000 human cells and 0.2-0.5 mg
of wet mouse and human tissues produced peptide samples sufficient
for multiple SWATH-MS analyses at optimal sample load applied to the
system. Generally, the reproducibility of the method increased with
decreasing tissue sample amounts. The SWATH maps acquired from
peptides derived from samples of varying sizes were essentially
identical based on the number, type, and quantity of identified
peptides. In conclusion, we determined the minimal sample required
for optimal PCT-SWATH analyses, and found smaller sample size
achieved higher quantitative accuracy.
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citation
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Shao S, Guo T, Koh C C, Gillessen S, Joerger M, Jochum W, Aebersold
R. Minimal sample requirement for highly multiplexed protein
quantification in cell lines and tissues by PCT-SWATH mass
spectrometry. Proteomics 2015; 15:3711-21.
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type
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journal paper/review (English)
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date of publishing
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10-09-2015
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journal title
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Proteomics (15/21)
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ISSN electronic
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1615-9861
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pages
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3711-21
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PubMed
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26287124
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DOI
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10.1002/pmic.201500161
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