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Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
Open accessAbstract
A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engine using a probabilistic scoring model. On proteome data, Andromeda performs as well as Mascot, a widely used commercial search engine, as judged by sensitivity and specificity analysis based on target decoy searches. Furthermore, it can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides, and accommodates extremely large databases. The algorithms of Andromeda are provided. Andromeda can function independently or as an integrated search engine of the widely used MaxQuant computational proteomics platform and both are freely available at www.maxquant.org. The combination enables analysis of large data sets in a simple analysis workflow on a desktop computer. For searching individual spectra Andromeda is also accessible via a web server. We demonstrate the flexibility of the system by implementing the capability to identify cofragmented peptides, significantly improving the total number of identified peptides.
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Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress
Cheng, Z., Teo, G., Krueger, S., Rock, T. M., Koh, H. W., Choi, H., & Vogel, C. (2016) · Molecular Systems Biology · doi:10.15252/msb.20156423 · Cited by 227
Extensive identification and analysis of conserved small ORFs in animals
Mackowiak, S. D., Zauber, H., Bielow, C., Thiel, D., Kutz, K., Calviello, L., Mastrobuoni, G., Rajewsky, N., Kempa, S., Selbach, M., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0742-x · Cited by 227
Sun, L., Zhu, G., Zhang, Z., Mou, S., & Dovichi, N. J. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00100 · Cited by 216
Tumour-selective activity of RAS-GTP inhibition in pancreatic cancer
Wasko, U. N., Jiang, J., Dalton, T. C., Curiel-Garcia, A., Edwards, A. C., Wang, Y., Lee, B., Orlen, M., Tian, S., Stalnecker, C. A., et al. (2024) · Nature · doi:10.1038/s41586-024-07379-z · Cited by 209
VDAC2 enables BAX to mediate apoptosis and limit tumor development
Chin, H. S., Li, M. X., Tan, I. K. L., Ninnis, R. L., Reljic, B., Scicluna, K., Dagley, L. F., Sandow, J. J., Kelly, G. L., Samson, A. L., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07309-4 · Cited by 196
A streamlined mass spectrometry–based proteomics workflow for large-scale FFPE tissue analysis
Coscia, F., Doll, S., Bech, J. M., Schweizer, L., Mund, A., Lengyel, E., Lindebjerg, J., Madsen, G. I., Moreira, J. M., & Mann, M. (2020) · The Journal of Pathology · doi:10.1002/path.5420 · Cited by 200
Self-citationJUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy
Wang, X., Li, Y., Wu, Z., Wang, H., Tan, H., & Peng, J. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.039586 · Cited by 194
A PP2A-B55 recognition signal controls substrate dephosphorylation kinetics during mitotic exit
Cundell, M. J., Hutter, L. H., Nunes Bastos, R., Poser, E., Holder, J., Mohammed, S., Novak, B., & Barr, F. A. (2016) · Journal of Cell Biology · doi:10.1083/jcb.201606033 · Cited by 193
Cell-Type-Resolved Quantitative Proteomics of Murine Liver
Azimifar, S. B., Nagaraj, N., Cox, J., & Mann, M. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.11.002 · Cited by 173
Self-citationAn evaluation of blood compatibility of silver nanoparticles
Huang, H., Lai, W., Cui, M., Liang, L., Lin, Y., Fang, Q., Liu, Y., & Xie, L. (2016) · Scientific Reports · doi:10.1038/srep25518 · Cited by 186
Zeiler, M., Straube, W. L., Lundberg, E., Uhlen, M., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.009613 · Cited by 168
Self-citationKinase-impaired BTK mutations are susceptible to clinical-stage BTK and IKZF1/3 degrader NX-2127
Montoya, S., Bourcier, J., Noviski, M., Lu, H., Thompson, M. C., Chirino, A., Jahn, J., Sondhi, A. K., Gajewski, S., Tan, Y. S. (., et al. (2024) · Science · doi:10.1126/science.adi5798 · Cited by 175
De novo derivation of proteomes from transcriptomes for transcript and protein identification
Evans, V. C., Barker, G., Heesom, K. J., Fan, J., Bessant, C., & Matthews, D. A. (2012) · Nature Methods · doi:10.1038/nmeth.2227 · Cited by 166
The neuropeptide complement of the marine annelid Platynereis dumerilii
Conzelmann, M., Williams, E. A., Krug, K., Franz-Wachtel, M., Macek, B., & Jékely, G. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-906 · Cited by 165
Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance
Fazakerley, D. J., Chaudhuri, R., Yang, P., Maghzal, G. J., Thomas, K. C., Krycer, J. R., Humphrey, S. J., Parker, B. L., Fisher-Wellman, K. H., Meoli, C. C., et al. (2018) · eLife · doi:10.7554/elife.32111 · Cited by 160
Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database
Schaab, C., Geiger, T., Stoehr, G., Cox, J., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.014068 · Cited by 164
Self-citationAn automated pipeline for high-throughput label-free quantitative proteomics
Weisser, H., Nahnsen, S., Grossmann, J., Nilse, L., Quandt, A., Brauer, H., Sturm, M., Kenar, E., Kohlbacher, O., Aebersold, R., et al. (2013) · Journal of Proteome Research · doi:10.1021/pr300992u · Cited by 160
Characterization of the E. coli proteome and its modifications during growth and ethanol stress
Soufi, B., Krug, K., Harst, A., & Macek, B. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00103 · Cited by 142
AIM2 inflammasome is activated by pharmacological disruption of nuclear envelope integrity
Di Micco, A., Frera, G., Lugrin, J., Jamilloux, Y., Hsu, E.-T., Tardivel, A., De Gassart, A., Zaffalon, L., Bujisic, B., Siegert, S., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1602419113 · Cited by 143
The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis
Solans, L., Gonzalo-Asensio, J., Sala, C., Benjak, A., Uplekar, S., Rougemont, J., Guilhot, C., Malaga, W., Martín, C., & Cole, S. T. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004183 · Cited by 147
A multiregional proteomic survey of the postnatal human brain
Carlyle, B. C., Kitchen, R. R., Kanyo, J. E., Voss, E. Z., Pletikos, M., Sousa, A. M. M., Lam, T. T., Gerstein, M. B., Sestan, N., & Nairn, A. C. (2017) · Nature Neuroscience · doi:10.1038/s41593-017-0011-2 · Cited by 143
Pelka, K., Bertheloot, D., Reimer, E., Phulphagar, K., Schmidt, S. V., Christ, A., Stahl, R., Watson, N., Miyake, K., Hacohen, N., et al. (2018) · Immunity · doi:10.1016/j.immuni.2018.04.011 · Cited by 145
Metadata
- Authors
- Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., & Mann, M.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2011-04
- Volume
- 10
- Issue
- 4
- Pages
- 1794-1805
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W2036321220
- Cited by
- 5,500
- References
- 7
- FWCI
- 81.12
- Type
- journal article
- Language
- en
- Open access
- hybrid
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.
