High-throughput proteomics of nanogram-scale samples with Zeno SWATH MS
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
- Core Facility – High-Throughput Mass Spectrometry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Core Facility – High-Throughput Mass Spectrometry, Germany
- Sciex, Canada
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, United Kingdom
Figures
Figure 1 with 2 supplements
Comparison between SWATH and Zeno SWATH MS in proteome coverage and quantification precision and using 5 µl/min, 20 min micro-flow-rate chromatography.
(a,b) Reproducibility of protein identification using SWATH MS and Zeno SWATH MS on human cell line standard (K562) separated by micro-flow chromatography with a 62.5 ng load. Average identification …
Figure 1—figure supplement 1
The ZenoTOF structure and Zeno Trap used in Zeno SWATH.
(a) Expanded view of the Zeno trap – a linear ion trap introduced after the collision cell (Q2). When enabled, all fragment ions in the selected mass range are trapped in an axial pseudopotential …
Figure 1—figure supplement 2
Comparison between SWATH MS and Zeno SWATH MS in quantification precision with two-species proteome mixture analysis.
(a) Protein-level LFQbench results for SWATH MS. (b) Precursor-level LFQbench results for SWATH MS. (c) Precursor-level LFQbench results for Zeno SWATH MS upon the separation of 1 µl injection of …
Figure 2 with 1 supplement
Zeno SWATH MS and its performance on K562 human cell line standard using 5 µl/min, 20 min micro-flow chromatography (SWATH MS on the TripleTOF 6600 system [blue], SWATH MS on the ZenoTOF 7600 system [yellow], and Zeno SWATH MS on the ZenoTOF 7600 system [red]).
(a) Precursor identification performance using SWATH and Zeno SWATH. Illustrated is the average number of precursors identified (n=3, error bars [±1 SD] shown in plot) for a K562 standard dilution …
Figure 2—figure supplement 1
Zeno SWATH MS and its performance on the K562 human cell line standard using 5 µl/min, 20 min micro-flow chromatography (SWATH MS on the TripleTOF 6600 system [blue], SWATH MS on the ZenoTOF 7600 system [yellow], and Zeno SWATH MS [red]).
(a) Protein identification performance using SWATH and Zeno SWATH MS. Illustrated is the average number of proteins identified (n=3, error bars [±1 SD]) for a K562 human cell line standard dilution …
Figure 3 with 1 supplement
Protein identification performance on K562 human cell line standard using 800 µl/min, 5 min gradient chromatography in SWATH and Zeno SWATH MS.
(a) Comparison of sample injection amount and identification performance with SWATH and Zeno SWATH MS. Illustrated is the average number of proteins identified (n=3, error bars [±1 SD] shown in …
Figure 3—figure supplement 1
Precursor identification performance on K562 human cell line standard using 800 µl/min, 5 min gradient chromatography in SWATH and Zeno SWATH MS.
(a) Comparison of sample injection amount and precursor identification performance with SWATH and Zeno SWATH MS. Illustrated is the average number of precursors identified (n=3, error bars [±1 SD] …
Figure 4 with 1 supplement
Protein identification number with SWATH MS and Zeno SWATH MS in different sample types with 5 µl/min, 20 min micro-flow-rate chromatography.
We generated tryptic digests from human plasma, and protein extracts from the yeast Saccharomyces cerevisiae S228c, the Escherichia coli lab strain K-12, and chickpea (Cicer arietinum) seedlings …
Figure 4—figure supplement 1
Precursor identification with SWATH acquisition and Zeno SWATH MS in different sample types with 5 µl/min, 20 min micro-flow-rate chromatography.
We generated tryptic digests from human plasma, and protein extracts from the yeast Saccharomyces cerevisiae S288c, the Escherichia coli lab strain K-12, and chickpea (Cicer arietinum) seedlings …
Figure 5
Precursor and protein identification performance with 100 ng K562 human cell line lysate injection using 5 µl/min, 20 min micro-flow chromatography coupled with different SWATH window number acquisition schemes.
For the 40 variable window SWATH acquisition scheme, 26,115 precursors from 3904 proteins were identified; the 60 variable window SWATH acquisition scheme identified 25,884 precursors from 4025 …
Additional files
-
Supplementary file 1
Precursors and proteins identification number in all sample species – precursors identification.
- https://cdn.elifesciences.org/articles/83947/elife-83947-supp1-v1.xlsx
-
Supplementary file 2
LC-MS instrumentation parameters.
- https://cdn.elifesciences.org/articles/83947/elife-83947-supp2-v1.xlsx
-
MDAR checklist
- https://cdn.elifesciences.org/articles/83947/elife-83947-mdarchecklist1-v1.docx
