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The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

Tyanova, Stefka, Temu, Tikira, Cox, Juergen·2016·Nature Protocols

DOI 10.1038/nprot.2016.136

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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
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Global quantification of mammalian gene expression control
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“44| Set the minimum FDR at which a protein group should be accepted.”
Background
Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ
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Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
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Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins
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A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards
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More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS
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Self-citation
Increasing the Multiplexing Capacity of TMTs Using Reporter Ion Isotopologues with Isobaric Masses
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Li, Y., Xu, C., Wang, B., Xu, F., Ma, F., Qu, Y., Jiang, D., Li, K., Feng, J., Tian, S., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33282-0 · Cited by 80
Proteome Profiling of 1 to 5 Spiked Circulating Tumor Cells Isolated from Whole Blood Using Immunodensity Enrichment, Laser Capture Microdissection, Nanodroplet Sample Processing, and Ultrasensitive nanoLC–MS
Zhu, Y., Podolak, J., Zhao, R., Shukla, A. K., Moore, R. J., Thomas, G. V., & Kelly, R. T. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b03268 · Cited by 75
The link between amyloid β and ferroptosis pathway in Alzheimer’s disease progression
Majerníková, N., Marmolejo-Garza, A., Salinas, C. S., Luu, M. D. A., Zhang, Y., Trombetta-Lima, M., Tomin, T., Birner-Gruenberger, R., Lehtonen, Š., Koistinaho, J., et al. (2024) · Cell Death & Disease · doi:10.1038/s41419-024-07152-0 · Cited by 73
The interaction network of the YidC insertase with the SecYEG translocon, SRP and the SRP receptor FtsY
Petriman, N.-A., Jauß, B., Hufnagel, A., Franz, L., Sachelaru, I., Drepper, F., Warscheid, B., & Koch, H.-G. (2018) · Scientific Reports · doi:10.1038/s41598-017-19019-w · Cited by 66
Surface Proteomics Reveals CD72 as a Target for In Vitro –Evolved Nanobody-Based CAR-T Cells in KMT2A/MLL1 -Rearranged B-ALL
Nix, M. A., Mandal, K., Geng, H., Paranjape, N., Lin, Y.-H. T., Rivera, J. M., Marcoulis, M., White, K. L., Whitman, J. D., Bapat, S. P., et al. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-0242 · Cited by 72
Large neutral amino acid levels tune perinatal neuronal excitability and survival
Knaus, L. S., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., Gorkiewicz, S., Amberg, N., Pauler, F. M., Knittl-Frank, C., et al. (2023) · Cell · doi:10.1016/j.cell.2023.02.037 · Cited by 70
In Vitro Kinase-to-Phosphosite Database (iKiP-DB) Predicts Kinase Activity in Phosphoproteomic Datasets
Mari, T., Mösbauer, K., Wyler, E., Landthaler, M., Drosten, C., & Selbach, M. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00198 · Cited by 70
A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair
van den Heuvel, D., Spruijt, C. G., González-Prieto, R., Kragten, A., Paulsen, M. T., Zhou, D., Wu, H., Apelt, K., van der Weegen, Y., Yang, K., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21520-w · Cited by 70
A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair
van den Heuvel, D., Spruijt, C. G., González-Prieto, R., Kragten, A., Paulsen, M. T., Zhou, D., Wu, H., Apelt, K., van der Weegen, Y., Yang, K., et al. (2020) · doi:10.1101/2020.01.04.894808 · Cited by 69
Urine proteome of COVID-19 patients
(2020) · doi:10.1016/j.urine.2021.02.001 · Cited by 68
Decoupling of Rates of Protein Synthesis from Cell Expansion Leads to Supergrowth
Knapp, B. D., Odermatt, P., Rojas, E. R., Cheng, W., He, X., Huang, K. C., & Chang, F. (2019) · Cell Systems · doi:10.1016/j.cels.2019.10.001 · Cited by 68
Integrative proteogenomic characterization of early esophageal cancer
Li, L., Jiang, D., Zhang, Q., Liu, H., Xu, F., Guo, C., Qin, Z., Wang, H., Feng, J., Liu, Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37440-w · Cited by 67
Population-scale proteome variation in human induced pluripotent stem cells
(2020) · doi:10.7554/elife.57390 · Cited by 59
The N-cadherin interactome in primary cardiomyocytes as defined using quantitative proximity proteomics
Li, Y., Merkel, C. D., Zeng, X., Heier, J. A., Cantrell, P. S., Sun, M., Stolz, D. B., Watkins, S. C., Yates, N. A., & Kwiatkowski, A. V. (2019) · Journal of Cell Science · doi:10.1242/jcs.221606 · Cited by 58
Unexpected complexity of the ammonia monooxygenase in archaea
(2023) · doi:10.1038/s41396-023-01367-3 · Cited by 58
A deeper look at carrier proteome effects for single-cell proteomics
Ye, Z., Batth, T. S., Rüther, P., & Olsen, J. V. (2022) · Communications Biology · doi:10.1038/s42003-022-03095-4 · Cited by 55
Nanoproteomics comes of age
Zhu, Y., Piehowski, P. D., Kelly, R. T., & Qian, W.-J. (2018) · Expert Review of Proteomics · doi:10.1080/14789450.2018.1537787 · Cited by 50
Inferring protein-protein interaction networks from mass spectrometry-based proteomic approaches: a mini-review
Yugandhar, K., Gupta, S., & Yu, H. (2019) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2019.05.007 · Cited by 51
“…tools for processing large-scale SILAC datasets [61], along with Census [51,62], pQuant [63], TPP [64], IsoQuant [65] etc. MaxQuant utilizes Andromeda search engine that incorporates length, charge and number of modi ﬁ cations of the peptides for quality peptide spectrum match (PSM) scoring [66].”
Method
Multilevel proteomic analyses reveal molecular diversity between diffuse-type and intestinal-type gastric cancer
Shi, W., Wang, Y., Xu, C., Li, Y., Ge, S., Bai, B., Zhang, K., Wang, Y., Zheng, N., Wang, J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-35797-6 · Cited by 50
Whey Peptides Stimulate Differentiation and Lipid Metabolism in Adipocytes and Ameliorate Lipotoxicity-Induced Insulin Resistance in Muscle Cells
D’Souza, K., Mercer, A., Mawhinney, H., Pulinilkunnil, T., Udenigwe, C. C., & Kienesberger, P. C. (2020) · Nutrients · doi:10.3390/nu12020425 · Cited by 47
Hepatitis B virus Core protein nuclear interactome identifies SRSF10 as a host RNA-binding protein restricting HBV RNA production
Chabrolles, H., Auclair, H., Vegna, S., Lahlali, T., Pons, C., Michelet, M., Couté, Y., Belmudes, L., Chadeuf, G., Kim, Y., et al. (2020) · PLOS Pathogens · doi:10.1371/journal.ppat.1008593 · Cited by 48
Single‐cell proteomics differentiates Arabidopsis root cell types
Montes, C., Zhang, J., Nolan, T. M., & Walley, J. W. (2024) · New Phytologist · doi:10.1111/nph.19923 · Cited by 48
Metagenomics combined with activity-based proteomics point to gut bacterial enzymes that reactivate mycophenolate
(2022) · doi:10.1080/19490976.2022.2107289 · Cited by 45
Noncompetitive binding of PpiD and YidC to the SecYEG translocon expands the global view on the SecYEG interactome in Escherichia coli
Jauss, B., Petriman, N.-A., Drepper, F., Franz, L., Sachelaru, I., Welte, T., Steinberg, R., Warscheid, B., & Koch, H.-G. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.010686 · Cited by 43
An accessible workflow for high-sensitivity proteomics using parallel accumulation-serial fragmentation (PASEF)
Skowronek, P., Wallmann, G., Wahle, M., Willems, S., & Mann, M. (2025) · Nature Protocols · doi:10.1038/s41596-024-01104-w · Cited by 43
AMPK-dependent activation of the Cyclin Y/CDK16 complex controls autophagy
Dohmen, M., Krieg, S., Agalaridis, G., Zhu, X., Shehata, S. N., Pfeiffenberger, E., Amelang, J., Bütepage, M., Buerova, E., Pfaff, C. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14812-0 · Cited by 40
A modified TurboID approach identifies tissue-specific centriolar components in C. elegans
Holzer, E., Rumpf-Kienzl, C., Falk, S., & Dammermann, A. (2022) · PLOS Genetics · doi:10.1371/journal.pgen.1010150 · Cited by 37
Proteolysis in Irish farmhouse Camembert cheese during ripening
Mane, A., & McSweeney, P. L. H. (2020) · Journal of Food Biochemistry · doi:10.1111/jfbc.13101 · Cited by 35
The First Whole-Cell Proteome- and Lysine-Acetylome-Based Comparison between Trichophyton rubrum Conidial and Mycelial Stages
Xu, X., Liu, T., Yang, J., Chen, L., Liu, B., Wang, L., & Jin, Q. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00793 · Cited by 36
TREX reveals proteins that bind to specific RNA regions in living cells
(2024) · doi:10.1038/s41592-024-02181-1 · Cited by 36
Purification of functional Plasmodium falciparum tubulin allows for the identification of parasite-specific microtubule inhibitors
Hirst, W. G., Fachet, D., Kuropka, B., Weise, C., Saliba, K. J., & Reber, S. (2022) · Current Biology · doi:10.1016/j.cub.2021.12.049 · Cited by 35
The aged hematopoietic system promotes hippocampal‐dependent cognitive decline
Smith, L. K., Verovskaya, E., Bieri, G., Horowitz, A. M., von Ungern‐Sternberg, S. N. I., Lin, K., Seizer, P., Passegué, E., & Villeda, S. A. (2020) · Aging Cell · doi:10.1111/acel.13192 · Cited by 31
A short dasatinib and quercetin treatment is sufficient to reinstate potent adult neuroregenesis in the aged killifish
Van houcke, J., Mariën, V., Zandecki, C., Ayana, R., Pepermans, E., Boonen, K., Seuntjens, E., Baggerman, G., & Arckens, L. (2023) · npj Regenerative Medicine · doi:10.1038/s41536-023-00304-4 · Cited by 29
Bacterial Longevity Requires Protein Synthesis and a Stringent Response
Yin, L., Ma, H., Nakayasu, E. S., Payne, S. H., Morris, D. R., & Harwood, C. S. (2019) · mBio · doi:10.1128/mbio.02189-19 · Cited by 31
Cardiopoietic stem cell therapy restores infarction-altered cardiac proteome
Arrell, D. K., Rosenow, C. S., Yamada, S., Behfar, A., & Terzic, A. (2020) · npj Regenerative Medicine · doi:10.1038/s41536-020-0091-6 · Cited by 30
Human cerebrospinal fluid contains diverse lipoprotein subspecies enriched in proteins implicated in central nervous system health
Merrill, N. J., Davidson, W. S., He, Y., Díaz Ludovico, I., Sarkar, S., Berger, M. R., McDermott, J. E., Van Eldik, L. J., Wilcock, D. M., Monroe, M. E., et al. (2023) · Science Advances · doi:10.1126/sciadv.adi5571 · Cited by 27
A desert Chlorella sp. that thrives at extreme high‐light intensities using a unique photoinhibition protection mechanism
Levin, G., Yasmin, M., Liveanu, V., Burstein, C., Hanna, R., Kleifeld, O., Simanowitz, M. C., Meir, A., Tadmor, Y., Hirschberg, J., et al. (2023) · The Plant Journal · doi:10.1111/tpj.16241 · Cited by 27
Integrative multi-omic analysis reveals conserved cell-projection deficits in human Down syndrome brains
Rastogi, M., Bartolucci, M., Nanni, M., Aloisio, M., Vozzi, D., Petretto, A., Contestabile, A., & Cancedda, L. (2024) · Neuron · doi:10.1016/j.neuron.2024.05.002 · Cited by 26
Germ cell-specific eIF4E1b regulates maternal mRNA translation to ensure zygotic genome activation
Yang, G., Xin, Q., Feng, I., Wu, D., & Dean, J. (2023) · Genes & Development · doi:10.1101/gad.350400.123 · Cited by 25
Rescue of Escherichia coli auxotrophy by de novo small proteins
Babina, A. M., Surkov, S., Ye, W., Jerlström-Hultqvist, J., Larsson, M., Holmqvist, E., Jemth, P., Andersson, D. I., & Knopp, M. (2023) · eLife · doi:10.7554/elife.78299 · Cited by 24
Condensin II activation by M18BP1
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RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells
Durand, S., Bruelle, M., Bourdelais, F., Bennychen, B., Blin-Gonthier, J., Isaac, C., Huyghe, A., Martel, S., Seyve, A., Vanbelle, C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36037-7 · Cited by 21
Biomarkers in a socially exchanged fluid reflect colony maturity, behavior, and distributed metabolism
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Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny
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Assembly and disassembly of Aspergillus fumigatus conidial rodlets
Valsecchi, I., Lai, J. I., Stephen-Victor, E., Pillé, A., Beaussart, A., Lo, V., Pham, C. L. L., Aimanianda, V., Kwan, A. H., Duchateau, M., et al. (2019) · The Cell Surface · doi:10.1016/j.tcsw.2019.100023 · Cited by 46
The plastoglobule-localized protein AtABC1K6 is a Mn2+-dependent kinase necessary for timely transition to reproductive growth
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Pupylation-based proximity labeling reveals regulatory factors in cellulose biosynthesis in Arabidopsis
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Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis
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RNA to Rule Them All: Critical Steps in Lassa Virus Ribonucleoparticle Assembly and Recruitment
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Mmp14 is required for matrisome homeostasis and circadian rhythm in fibroblasts
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Authors: Tyanova, S., Temu, T., & Cox, J.
Venue: Nature Protocols
Publisher: Springer Science and Business Media LLC
Published: 2016-10-27
Volume: 11
Issue: 12
Pages: 2301-2319
ISSN: 1750-2799 (ISSN-L)
1754-2189
DOI: 10.1038/nprot.2016.136
OpenAlex: W2544360569
Cited by: 4,797
References: 14
FWCI: 86.78
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)

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