The DOI matches its Crossref record; 22 of the 22 references it cites were found in a registry or an index.
Consecutive Proteolytic Digestion in an Enzyme Reactor Increases Depth of Proteomic and Phosphoproteomic Analysis
Open accessAbstract
Analytical advantages of using multiple enzymes for sample digestion (MED), primarily an increase of sequence coverage, have been reported in several studies. However, this approach is only rarely used, mainly because it requires additional sample and mass spectrometric measurement time. We have previously described Filter Aided Sample Preparation (FASP), a type of proteomic reactor, in which samples dissolved in sodium dodecyl sulfate (SDS) are digested in an ultrafiltration unit. In FASP, such as in any other preparation protocol, a portion of sample remains after digestion and peptide elution. Making use of this fact, we here develop a protocol enabling consecutive digestion of the sample with two or three enzymes. By use of the FASP method, peptides are liberated after each digestion step and remaining material is subsequently cleaved with the next proteinase. We observed excellent performance of the ultrafiltration devices in this mode, allowing efficient separation of orthogonal populations of peptides, resulting in an increase in the numbers of identified peptides and proteins. At the low microgram level, we found that the consecutive use of endoproteinases LysC and trypsin enabled identification of up to 40% more proteins and phosphorylation sites in comparison to the commonly used one-step tryptic digestion. MED-FASP offers efficient exploration of previously unused sample material, increasing depth of proteomic analyses and sequence coverage.
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Citations
Cites
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
Self-citationMass Spectrometric Sequencing of Proteins from Silver-Stained Polyacrylamide Gels
Shevchenko, A., Wilm, M., Vorm, O., & Mann, M. (1996) · Analytical Chemistry · doi:10.1021/ac950914h · Cited by 8,995
Self-citationUniversal sample preparation method for proteome analysis
Wiśniewski, J. R., Zougman, A., Nagaraj, N., & Mann, M. (2009) · Nature Methods · doi:10.1038/nmeth.1322 · Cited by 8,352
Self-citationAndromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., & Mann, M. (2011) · Journal of Proteome Research · doi:10.1021/pr101065j · Cited by 5,500
Self-citationLarsen, M. R., Thingholm, T. E., Jensen, O. N., Roepstorff, P., & Jørgensen, T. J. D. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.t500007-mcp200 · Cited by 1,476
Higher-energy C-trap dissociation for peptide modification analysis
Olsen, J. V., Macek, B., Lange, O., Makarov, A., Horning, S., & Mann, M. (2007) · Nature Methods · doi:10.1038/nmeth1060 · Cited by 999
Self-citationPrecision Mapping of an In Vivo N-Glycoproteome Reveals Rigid Topological and Sequence Constraints
Zielinska, D. F., Gnad, F., Wiśniewski, J. R., & Mann, M. (2010) · Cell · doi:10.1016/j.cell.2010.04.012 · Cited by 902
Self-citationWiśniewski, J. R., Zougman, A., & Mann, M. (2009) · Journal of Proteome Research · doi:10.1021/pr900748n · Cited by 545
Self-citationValue of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics
Swaney, D. L., Wenger, C. D., & Coon, J. J. (2010) · Journal of Proteome Research · doi:10.1021/pr900863u · Cited by 474
Sample preparation and digestion for proteomic analyses using spin filters
Manza, L. L., Stamer, S. L., Ham, A. L., Codreanu, S. G., & Liebler, D. C. (2005) · PROTEOMICS · doi:10.1002/pmic.200401063 · Cited by 382
Cited by
Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes
Vlastaridis, P., Kyriakidou, P., Chaliotis, A., Van de Peer, Y., Oliver, S. G., & Amoutzias, G. D. (2017) · GigaScience · doi:10.1093/gigascience/giw015 · Cited by 733
A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards
Wiśniewski, J. R., Hein, M. Y., Cox, J., & Mann, M. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.037309 · Cited by 690
Self-citationGlatter, T., Ludwig, C., Ahrné, E., Aebersold, R., Heck, A. J. R., & Schmidt, A. (2012) · Journal of Proteome Research · doi:10.1021/pr300273g · Cited by 364
Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling
Riley, N. M., & Coon, J. J. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.5b04123 · Cited by 265
Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma
Wiśniewski, J. R., Ostasiewicz, P., Duś, K., Zielińska, D. F., Gnad, F., & Mann, M. (2012) · Molecular Systems Biology · doi:10.1038/msb.2012.44 · Cited by 248
Self-citationWalerych, D., Lisek, K., Sommaggio, R., Piazza, S., Ciani, Y., Dalla, E., Rajkowska, K., Gaweda-Walerych, K., Ingallina, E., Tonelli, C., et al. (2016) · Nature Cell Biology · doi:10.1038/ncb3380 · Cited by 239
Self-citationWiśniewski, J. R., Vildhede, A., Norén, A., & Artursson, P. (2016) · Journal of Proteomics · doi:10.1016/j.jprot.2016.01.016 · Cited by 185
Self-citationMamczur, P., Borsuk, B., Paszko, J., Sas, Z., Mozrzymas, J., Wiśniewski, J. R., Gizak, A., & Rakus, D. (2015) · Glia · doi:10.1002/glia.22753 · Cited by 71
Self-citationIlluminating the function of the orphan transporter, SLC22A10, in humans and other primates
Yee, S. W., Ferrández-Peral, L., Alentorn-Moron, P., Fontsere, C., Ceylan, M., Koleske, M. L., Handin, N., Artegoitia, V. M., Lara, G., Chien, H.-C., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48569-7 · Cited by 4
Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates
Giacomini, K., Yee, S. W., Ferrández-Peral, L., Alentorn, P., Fontsere, C., Ceylan, M., Koleske, M., Handin, N., Artegoitia, V., Lara, G., et al. (2023) · doi:10.21203/rs.3.rs-3263845/v1 · Cited by 1
Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates
(2023) · doi:10.1101/2023.08.08.552553
Metadata
- Authors
- Wiśniewski, J. R., & Mann, M.
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-03-01
- Volume
- 84
- Issue
- 6
- Pages
- 2631-2637
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- OpenAlex
- W2276896823
- Cited by
- 299
- References
- 22
- FWCI
- 9.31
- Type
- journal article
- Language
- en
- Open access
- green
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