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Stop and Go Extraction Tips for Matrix-Assisted Laser Desorption/Ionization, Nanoelectrospray, and LC/MS Sample Pretreatment in Proteomics
Abstract
Proteomics is critically dependent on optimal sample preparation. Particularly, the interface between protein digestion and mass spectrometric analysis has a large influence on the overall quality and sensitivity of the analysis. We here describe a novel procedure in which a very small disk of beads embedded in a Teflon meshwork is placed as a microcolumn into pipet tips. Termed Stage, for STop And Go Extraction, the procedure has been implemented with commercially available material (C18 Empore Disks (3M, Minneapolis, MN)) as frit and separation material. The disk is introduced in a simple and fast process yielding a convenient and completely reliable procedure for the production of self-packed microcolumns in pipet tips. It is held in place free of obstacles solely by the narrowing tip, ensuring optimized loading and elution of analytes. Five disks are conveniently placed in 1 min, adding <0.1 cent in material costs to the price of each tip. The system allows fast loading with low backpressure (>300 micro/min for the packed column using manual force) while eliminating the possibility of blocking. The loading capacity of C18-StageTips (column bed: 0.4 mm diameter, 0.5 mm length) is 2-4 microg of protein digest, which can be increased by using larger diameter or stacked disks. Five femtomole of tryptic BSA digest could be recovered quantitatively. We have found that the Stage system is well-suited as a universal sample preparation system for proteomics.
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Du, Y., Li, H., Shao, J., Wu, T., Xu, W., Hu, X., & Chen, J. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.878874 · Cited by 45
Promotion of Myoblast Differentiation by Fkbp5 via Cdk4 Isomerization
Ruiz-Estevez, M., Staats, J., Paatela, E., Munson, D., Katoku-Kikyo, N., Yuan, C., Asakura, Y., Hostager, R., Kobayashi, H., Asakura, A., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.11.006 · Cited by 39
“1% trifluoroacetic acid in water, cleaned with the Stage Tip protocol (Rappsilber et al., 2003), and dried in vacuo.”
MethodGerovac, M., Wicke, L., Chihara, K., Schneider, C., Lavigne, R., & Vogel, J. (2021) · mBio · doi:10.1128/mbio.03454-20 · Cited by 40
Quantitative measurement of allele‐specific protein expression in a diploid yeast hybrid by LC‐MS
Khan, Z., Bloom, J. S., Amini, S., Singh, M., Perlman, D. H., Caudy, A. A., & Kruglyak, L. (2012) · Molecular Systems Biology · doi:10.1038/msb.2012.34 · Cited by 37
Substrate specificity of the TRAMP nuclear surveillance complexes
Delan-Forino, C., Spanos, C., Rappsilber, J., & Tollervey, D. (2020) · Nature Communications · doi:10.1038/s41467-020-16965-4 · Cited by 36
Self-citationUnbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics
Steger, M., Nishiguchi, G., Wu, Q., Schwalb, B., Shashikadze, B., McGowan, K., Actis, M., Aggarwal, A., Shi, Z., Price, J., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-62829-0 · Cited by 32
Syred, H. M., Welburn, J., Rappsilber, J., & Ohkura, H. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.028563 · Cited by 25
Self-citationZinnall, U., Milek, M., Minia, I., Vieira-Vieira, C. H., Müller, S., Mastrobuoni, G., Hazapis, O.-G., Del Giudice, S., Schwefel, D., Bley, N., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30322-7 · Cited by 30
Proteomic Analyses Identify a Novel Role for EZH2 in the Initiation of Cancer Cell Drug Tolerance
Pham, V., Pitti, R., Tindell, C. A., Cheung, T. K., Masselot, A., Stephan, J.-P., Guler, G. D., Wilson, C., Lill, J., Arnott, D., et al. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00773 · Cited by 26
Canestrari, J. G., Lasek‐Nesselquist, E., Upadhyay, A., Rofaeil, M., Champion, M. M., Wade, J. T., Derbyshire, K. M., & Gray, T. A. (2020) · Molecular Microbiology · doi:10.1111/mmi.14498 · Cited by 25
Milligan, L., Sayou, C., Tuck, A., Auchynnikava, T., Reid, J. E., Alexander, R., Alves, F. D. L., Allshire, R., Spanos, C., Rappsilber, J., et al. (2017) · eLife · doi:10.7554/elife.27082 · Cited by 23
Self-citationMapping the invisible chromatin transactions of prophase chromosome remodeling
Samejima, I., Spanos, C., Samejima, K., Rappsilber, J., Kustatscher, G., & Earnshaw, W. C. (2022) · Molecular Cell · doi:10.1016/j.molcel.2021.12.039 · Cited by 21
Self-citationYaseen, I., White, S. A., Torres-Garcia, S., Spanos, C., Lafos, M., Gaberdiel, E., Yeboah, R., El Karoui, M., Rappsilber, J., Pidoux, A. L., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00801-y · Cited by 20
Self-citationLevy-Myers, R., Daudelin, D., Na, C. H., & Sockanathan, S. (2023) · Science Advances · doi:10.1126/sciadv.adg2067 · Cited by 15
An NADH-controlled gatekeeper of ATP synthase
Schildhauer, F., Ryl, P. S. J., Lauer, S. M., Lenz, S., Barlas, A. B., Ouzounidis, V. R., Jeffrey, K., Marcu, D.-C., O’Reilly, F. J., Graziadei, A., et al. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.06.007 · Cited by 11
Self-citationStructural mechanism of CRL4‐instructed STAT2 degradation via a novel cytomegaloviral DCAF receptor
Le‐Trilling, V. T. K., Banchenko, S., Paydar, D., Leipe, P. M., Binting, L., Lauer, S., Graziadei, A., Klingen, R., Gotthold, C., Bürger, J., et al. (2023) · The EMBO Journal · doi:10.15252/embj.2022112351 · Cited by 10
Self-citationThe Origin and Evolution of Sex Peptide and Sex Peptide Receptor Interactions
Peng, J., Svetec, N., Molina, H., & Zhao, L. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae065 · Cited by 9
Metadata
- Authors
- Rappsilber, J., Ishihama, Y., & Mann, M.
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2002-12-24
- Volume
- 75
- Issue
- 3
- Pages
- 663-670
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- OpenAlex
- W2003236418
- Cited by
- 2,644
- References
- 0
- FWCI
- 6.28
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
