Chem. J. Chinese Universities ›› 2024, Vol. 45 ›› Issue (11): 20240389.doi: 10.7503/cjcu20240389
• Review • Previous Articles
HUO Zhiyuan1,2, ZHOU Jinping3, MA Xiumin3(), ZHOU Yan1,2(
), HUANG Lin1,2(
)
Received:
2024-08-15
Online:
2024-11-10
Published:
2024-09-11
Contact:
MA Xiumin, ZHOU Yan, HUANG Lin
E-mail:maxiumin1210@sohu.com;zhouyan@shchest.org;linhuang@shsmu.edu.cn
Supported by:
CLC Number:
TrendMD:
HUO Zhiyuan, ZHOU Jinping, MA Xiumin, ZHOU Yan, HUANG Lin. Advances in Single-cell Multi-omics Analysis Based on Mass Spectrometry[J]. Chem. J. Chinese Universities, 2024, 45(11): 20240389.
1 | Baysoy A., Bai Z., Satija R., Fan R., Nat. Rev. Mol. Cell Biol., 2023, 24(10), 695—713 |
2 | Flynn E., Almonte⁃Loya A., Fragiadakis G. K., Annu. Rev. Biomed., 2023, 6(1), 313—337 |
3 | Macaulay I. C., Ponting C. P., Voet T., Trends Genet., 2017, 33(2), 155—168 |
4 | Zhu Q., Zhao X., Zhang Y., Li Y., Liu S., Han J., Sun Z., Wang C., Deng D., Wang S., Nat. Commun., 2023, 14(1), 8170 |
5 | Ma A., McDermaid A., Xu J., Chang Y., Ma Q., Trends Biotechnol., 2020, 38(9), 1007—1022 |
6 | Chen W., Yu H., Hao Y., Liu W., Wang R., Huang Y., Wu J., Feng L., Guan Y., Huang L., ACS Nano, 2023, 17(20), 19779—19792 |
7 | Wang Y., Xu X., Fang Y., Yang S., Wang Q., Liu W., Zhang J., Liang D., Zhai W., Qian K., ACS Nano, 2024, 18(3), 2409— 2420 |
8 | Wu J., Wei X., Gan J., Huang L., Shen T., Lou J., Liu B., Zhang J. X., Qian K., Adv. Funct. Mater., 2016, 26(22), 4016—4025 |
9 | Zhang J., Teng F., Hu B., Liu W., Huang Y., Wu J., Wang Y., Su H., Yang S., Zhang L., Adv. Mater., 2024, 36(18), 2311431 |
10 | Herzenberg L. A., Parks D., Sahaf B., Perez O., Roederer M., Herzenberg L. A., Clinical Chem., 2002, 48(10), 1819—1827 |
11 | Sherman S. E., Kuljanin M., Cooper T. T., Lajoie G. A., Hess D. A., Stem Cells Dev., 2020, 29(14), 895—910 |
12 | Melliou S., Diamandis P., Star Protoc., 2022, 3(4), 101774 |
13 | Espina V., Heiby M., Pierobon M., Liotta L. A., Expert Rev. Mol. Diagn., 2007, 7(5), 647—657 |
14 | Guise A. J., Misal S. A., Carson R., Chu J. H., Boekweg H., van Der Watt D., Welsh N. C., Truong T., Liang Y., Xu S., Benedetto G., Gagnon J., Payne S. H., Plowey E. D., Kelly R. T., Cell Rep., 2024, 43(1), 113636 |
15 | Rosenberger F. A., Thielert M., Strauss M. T., Schweizer L., Ammar C., Mädler S. C., Metousis A., Skowronek P., Wahle M., Madden K., Gote⁃Schniering J., Semenova A., Schiller H. B., Rodriguez E., Nordmann T. M., Mund A., Mann M., Nat. Methods, 2023, 20(10), 1530—1536 |
16 | Lecault V., White A. K., Singhal A., Hansen C. L., Curr. Opin. Chem. Biol., 2012, 16(3/4), 381—390 |
17 | Feng D., Li H., Xu T., Zheng F., Hu C., Shi X., Xu G., Anal. Chim. Acta, 2022, 1221, 340116 |
18 | Lamanna J., Scott E. Y., Edwards H. S., Chamberlain M. D., Dryden M. D. M., Peng J., Mair B., Lee A., Chan C., Sklavounos A. A., Heffernan A., Abbas F., Lam C., Olson M. E., Moffat J., Wheeler A. R., Nat. Commun., 2020, 11(1), 5632 |
19 | Misra B. B., Methods Mol. Biol., 2020, 2064, 191—217 |
20 | Cao Y. Q., Zhang L., Zhang J., Guo Y. L., Anal. Chem., 2020, 92(12), 8378—8385 |
21 | Duncan K. D., Fyrestam J., Lanekoff I., Analyst, 2019, 144(3), 782—793 |
22 | Hu K., Nguyen T. D. K., Rabasco S., Oomen P. E., Ewing A. G., Anal. Chem., 2020, 93(1), 41—71 |
23 | Lageveen⁃Kammeijer G. S. M., de Haan N., Mohaupt P., Wagt S., Filius M., Nouta J., Falck D., Wuhrer M., Nat. Commun., 2019, 10(1), 2137 |
24 | Oomen P. E., Aref M. A., Kaya I., Phan N. T. N., Ewing A. G., Anal. Chem., 2018, 91(1), 588—621 |
25 | Yin L., Zhang Z., Liu Y., Gao Y., Gu J., Analyst, 2019, 144(3), 824—845 |
26 | Qin S., Zhang Y., Shi M., Miao D., Lu J., Wen L., Bai Y., Nat. Commun., 2024, 15(1), 4387 |
27 | Shao Y., Zhou Y., Liu Y., Zhang W., Zhu G., Zhao Y., Zhang Q., Yao H., Zhao H., Guo G., Zhang S., Zhang X., Wang X., Chem. Sci., 2022, 13(27), 8065—8073 |
28 | Taylor M. J., Mattson S., Liyu A., Stopka S. A., Ibrahim Y. M., Vertes A., Anderton C. R., Metabolites, 2021, 11(4), 200 |
29 | Chen A., Yan M., Feng J., Bi L., Chen L., Hu S., Hong H., Shi L., Li G., Jin B., Zhang X., Wen L., IEEE T Bio⁃Med Eng., 2022, 69(1), 325—333 |
30 | Marques C., Friedrich F., Liu L., Castoldi F., Pietrocola F., Lanekoff I., J. Am. Soc. Mass Spectrom., 2023, 34(11), 2518—2524 |
31 | Zhang W., Xu F., Yao J., Mao C., Zhu M., Qian M., Hu J., Zhong H., Zhou J., Shi X., Chen Y., Nat. Commun., 2023, 14(1), 2485 |
32 | Cao J., Yao Q. J., Wu J., Chen X., Huang L., Liu W., Qian K., Wan J. J., Zhou B. O., Cell Metab., 2024, 36(1), 209—221 |
33 | Fuchs S., Sawas N., Staedler N., Schubert D. A., D'Andrea A., Zeiser R., Piali L., Hruz P., Frei A. P., Eur. J. Immunol., 2019, 49(3), 462—475 |
34 | Palii C. G., Cheng Q., Gillespie M. A., Shannon P., Mazurczyk M., Napolitani G., Price N. D., Ranish J. A., Morrissey E., Higgs D. R., Brand M., Cell Stem Cell, 2019, 24(5), 812—820 |
35 | Wang B., Wang Y., Chen Y., Gao M., Ren J., Guo Y., Situ C., Qi Y., Zhu H., Li Y., Guo X., Brief Bioinform., 2022, 23(4), bbac214 |
36 | Zhang Y., Mol. Cell. Proteomics, 2023, 22(7), 100583 |
37 | Petelski A. A., Slavov N., Specht H., Jove⁃J. Vis. Exp., 2022,(190), e63802 |
38 | Shen B., Pade L. R., Choi S. B., Muñoz⁃Llancao P., Manzini M. C., Nemes P., Front. Chem., 2022, 10, 863979 |
39 | Slavov N., Development, 2023, 150(13), dev201492 |
40 | Subrahmanyam P. B., Maecker H. T., Methods Mol. Biol., 2021, 2285, 49—63 |
41 | Naval P., Paneda L. P., Athanasopoulou M., Teppo J. S., Zubarev R. A., Vegvari A., Methods Mol. Biol., 2024, 2817, 133—143 |
42 | Huffman R. G., Leduc A., Wichmann C., di Gioia M., Borriello F., Specht H., Derks J., Khan S., Khoury L., Emmott E., Petelski A. A., Perlman D. H., Cox J., Zanoni I., Slavov N., Nat. Methods, 2023, 20(5), 714—722 |
43 | Yuan Z., Zhou Q., Cai L., Pan L., Sun W., Qumu S., Yu S., Feng J., Zhao H., Zheng Y., Shi M., Li S., Chen Y., Zhang X., Zhang M. Q., Nat. Methods, 2021, 18(10), 1223—1232 |
44 | Jiang Y. R., Zhu L., Cao L. R., Wu Q., Chen J. B., Wang Y., Wu J., Zhang T. Y., Wang Z. L., Guan Z. Y., Xu Q. Q., Fan Q. X., Shi S. W., Wang H. F., Pan J. Z., Fu X. D., Wang Y., Fang Q., Cell Rep., 2023, 42(11), 113455 |
45 | Mennillo E., Kim Y. J., Lee G., Rusu I., Patel R. K., Dorman L. C., Flynn E., Li S., Bain J. L., Andersen C., Rao A., Tamaki S., Tsui J., Shen A., Lotstein M. L., Rahim M., Naser M., Bernard⁃Vazquez F., Eckalbar W., Cho S. J., Beck K., El⁃Nachef N., Lewin S., Selvig D. R., Terdiman J. P., Mahadevan U., Oh D. Y., Fragiadakis G. K., Pisco A., Combes A. J., Kattah M. G., Nat. Commun., 2024, 15(1), 1493 |
46 | Wu J., Xu Q. Q., Jiang Y. R., Chen J. B., Ying W. X., Fan Q. X., Wang H. F., Wang Y., Shi S. W., Pan J. Z., Fang Q., Anal. Chem., 2024, 96(14), 5499—5508 |
47 | Zhao P., Feng Y., Wu J., Zhu J., Yang J., Ma X., Ouyang Z., Zhang X., Zhang W., Wang W., Anal. Chem., 2023, 95(18), 7212—7219 |
48 | Wagner J., Rapsomaniki M. A., Chevrier S., Anzeneder T., Langwieder C., Dykgers A., Rees M., Ramaswamy A., Muenst S., Soysal S. D., Cell, 2019, 177(5), 1330—1345 |
49 | Friebel E., Kapolou K., Unger S., Núñez N. G., Utz S., Rushing E. J., Regli L., Weller M., Greter M., Tugues S., Cell, 2020, 181(7), 1626—1642 |
50 | Guo Y., Cai L., Liu X., Ma L., Zhang H., Wang B., Qi Y., Liu J., Diao F., Sha J., Mol. Cell. Proteomics, 2022, 21(8), 100267 |
51 | Schoof E. M., Furtwängler B., Üresin N., Rapin N., Savickas S., Gentil C., Lechman E., Keller U. A. D., Dick J. E., Porse B. T., Nat. Commun., 2021, 12(1), 3341 |
52 | Brunner A. D., Thielert M., Vasilopoulou C., Ammar C., Coscia F., Mund A., Hoerning O. B., Bache N., Apalategui A., Lubeck M., Mol. Syst. Biol., 2022, 18(3), e10798 |
53 | Tsai A. G., Glass D. R., Juntilla M., Hartmann F. J., Oak J. S., Fernandez⁃Pol S., Ohgami R. S., Bendall S. C., Nat. Med., 2020, 26(3), 408—417 |
54 | Zhang L., Du F., Jin Q., Sun L., Wang B., Tan Z., Meng X., Huang B., Zhan Y., Su W., Adv. Sci., 2023, 10(35), 2300123 |
55 | Georg P., Astaburuaga⁃García R., Bonaguro L., Brumhard S., Michalick L., Lippert L. J., Kostevc T., Gäbel C., Schneider M., Streitz M., Cell, 2022, 185(3), 493—512 |
56 | Mogilenko D. A., Shpynov O., Andhey P. S., Arthur L., Swain A., Esaulova E., Brioschi S., Shchukina I., Kerndl M., Bambouskova M., Immunity, 2021, 54(1), 99—115 |
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