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For: Poulos RC, Hains PG, Shah R, Lucas N, Xavier D, Manda SS, Anees A, Koh JMS, Mahboob S, Wittman M, Williams SG, Sykes EK, Hecker M, Dausmann M, Wouters MA, Ashman K, Yang J, Wild PJ, deFazio A, Balleine RL, Tully B, Aebersold R, Speed TP, Liu Y, Reddel RR, Robinson PJ, Zhong Q. Strategies to enable large-scale proteomics for reproducible research. Nat Commun 2020;11:3793. [PMID: 32732981 PMCID: PMC7393074 DOI: 10.1038/s41467-020-17641-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 07/08/2020] [Indexed: 01/12/2023]  Open
Number Cited by Other Article(s)
1
Kardell O, Gronauer T, von Toerne C, Merl-Pham J, König AC, Barth TK, Mergner J, Ludwig C, Tüshaus J, Giesbertz P, Breimann S, Schweizer L, Müller T, Kliewer G, Distler U, Gomez-Zepeda D, Popp O, Qin D, Teupser D, Cox J, Imhof A, Küster B, Lichtenthaler SF, Krijgsveld J, Tenzer S, Mertins P, Coscia F, Hauck SM. Multicenter Longitudinal Quality Assessment of MS-Based Proteomics in Plasma and Serum. J Proteome Res 2025;24:1017-1029. [PMID: 39918541 PMCID: PMC11894660 DOI: 10.1021/acs.jproteome.4c00644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2024] [Revised: 12/14/2024] [Accepted: 01/15/2025] [Indexed: 03/08/2025]
2
Liu X, Sun H, Hou X, Sun J, Tang M, Zhang YB, Zhang Y, Sun W, Liu C. Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics. Nat Commun 2025;16:1051. [PMID: 39865094 PMCID: PMC11770173 DOI: 10.1038/s41467-025-56337-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 01/16/2025] [Indexed: 01/28/2025]  Open
3
Seo Y, Kang I, Lee HJ, Hwang J, Kwak SH, Oh MK, Lee H, Min H. Simple and robust high-throughput serum proteomics workflow with low-microflow LC-MS/MS. Anal Bioanal Chem 2024;416:7007-7018. [PMID: 39422715 PMCID: PMC11579186 DOI: 10.1007/s00216-024-05603-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 10/08/2024] [Accepted: 10/10/2024] [Indexed: 10/19/2024]
4
Cai Z, Apolinário S, Baião AR, Pacini C, Sousa MD, Vinga S, Reddel RR, Robinson PJ, Garnett MJ, Zhong Q, Gonçalves E. Synthetic augmentation of cancer cell line multi-omic datasets using unsupervised deep learning. Nat Commun 2024;15:10390. [PMID: 39614072 PMCID: PMC11607321 DOI: 10.1038/s41467-024-54771-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 11/18/2024] [Indexed: 12/01/2024]  Open
5
Liu Y, Mei L, Liang C, Zhong CQ, Tong M, Yu R. Cross-Run Hybrid Features Improve the Identification of Data-Independent Acquisition Proteomics. ACS OMEGA 2024;9:46362-46372. [PMID: 39583733 PMCID: PMC11579728 DOI: 10.1021/acsomega.4c07398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 09/25/2024] [Accepted: 10/02/2024] [Indexed: 11/26/2024]
6
Salahub C, Uhlmann J. Optimal Structured Matrix Approximation for Robustness to Incomplete Biosequence Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:2592-2597. [PMID: 38949937 DOI: 10.1109/tcbb.2024.3420903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
7
Tsantilas KA, Merrihew GE, Robbins JE, Johnson RS, Park J, Plubell DL, Canterbury JD, Huang E, Riffle M, Sharma V, MacLean BX, Eckels J, Wu CC, Bereman MS, Spencer SE, Hoofnagle AN, MacCoss MJ. A Framework for Quality Control in Quantitative Proteomics. J Proteome Res 2024;23:4392-4408. [PMID: 39248652 PMCID: PMC11973981 DOI: 10.1021/acs.jproteome.4c00363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
8
Yu Y, Mai Y, Zheng Y, Shi L. Assessing and mitigating batch effects in large-scale omics studies. Genome Biol 2024;25:254. [PMID: 39363244 PMCID: PMC11447944 DOI: 10.1186/s13059-024-03401-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/23/2024] [Indexed: 10/05/2024]  Open
9
Kohler D, Staniak M, Yu F, Nesvizhskii AI, Vitek O. An MSstats workflow for detecting differentially abundant proteins in large-scale data-independent acquisition mass spectrometry experiments with FragPipe processing. Nat Protoc 2024;19:2915-2938. [PMID: 38769142 DOI: 10.1038/s41596-024-01000-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/11/2024] [Indexed: 05/22/2024]
10
Ran P, Wang Y, Li K, He S, Tan S, Lv J, Zhu J, Tang S, Feng J, Qin Z, Li Y, Huang L, Yin Y, Zhu L, Yang W, Ding C. STAVER: a standardized benchmark dataset-based algorithm for effective variation reduction in large-scale DIA-MS data. Brief Bioinform 2024;25:bbae553. [PMID: 39504480 PMCID: PMC11540132 DOI: 10.1093/bib/bbae553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 09/12/2024] [Accepted: 10/19/2024] [Indexed: 11/08/2024]  Open
11
Rich JA, Fan Y, Chen Q, Meerzaman D, Stetler-Stevenson WG, Peeney D. Analysis of cancer cell line and tissue RNA sequencing data reveals an essential and dark matrisome. Matrix Biol Plus 2024;23:100156. [PMID: 39049902 PMCID: PMC11267082 DOI: 10.1016/j.mbplus.2024.100156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024]  Open
12
Fröhlich K, Fahrner M, Brombacher E, Seredynska A, Maldacker M, Kreutz C, Schmidt A, Schilling O. Data-Independent Acquisition: A Milestone and Prospect in Clinical Mass Spectrometry-Based Proteomics. Mol Cell Proteomics 2024;23:100800. [PMID: 38880244 PMCID: PMC11380018 DOI: 10.1016/j.mcpro.2024.100800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/08/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]  Open
13
Çelik MH, Gagneur J, Lim RG, Wu J, Thompson LM, Xie X. Identifying dysregulated regions in amyotrophic lateral sclerosis through chromatin accessibility outliers. HGG ADVANCES 2024;5:100318. [PMID: 38872308 PMCID: PMC11260578 DOI: 10.1016/j.xhgg.2024.100318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024]  Open
14
Bortel P, Hagn G, Skos L, Bileck A, Paulitschke V, Paulitschke P, Gleiter L, Mohr T, Gerner C, Meier-Menches SM. Memory effects of prior subculture may impact the quality of multiomic perturbation profiles. Proc Natl Acad Sci U S A 2024;121:e2313851121. [PMID: 38976734 PMCID: PMC11260104 DOI: 10.1073/pnas.2313851121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 06/03/2024] [Indexed: 07/10/2024]  Open
15
Humphries EM, Xavier D, Ashman K, Hains PG, Robinson PJ. High-Throughput Proteomics and Phosphoproteomics of Rat Tissues Using Microflow Zeno SWATH. J Proteome Res 2024;23:2355-2366. [PMID: 38819404 DOI: 10.1021/acs.jproteome.4c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
16
Calado CRC. Bridging the gap between target-based and phenotypic-based drug discovery. Expert Opin Drug Discov 2024;19:789-798. [PMID: 38747562 DOI: 10.1080/17460441.2024.2355330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 05/10/2024] [Indexed: 06/26/2024]
17
Webel H, Niu L, Nielsen AB, Locard-Paulet M, Mann M, Jensen LJ, Rasmussen S. Imputation of label-free quantitative mass spectrometry-based proteomics data using self-supervised deep learning. Nat Commun 2024;15:5405. [PMID: 38926340 PMCID: PMC11208500 DOI: 10.1038/s41467-024-48711-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/13/2024] [Indexed: 06/28/2024]  Open
18
Padhye BD, Nawaz U, Hains PG, Reddel RR, Robinson PJ, Zhong Q, Poulos RC. Proteomic insights into paediatric cancer: Unravelling molecular signatures and therapeutic opportunities. Pediatr Blood Cancer 2024;71:e30980. [PMID: 38556739 DOI: 10.1002/pbc.30980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/02/2024]
19
Pelletier SJ, Leclercq M, Roux-Dalvai F, de Geus MB, Leslie S, Wang W, Lam TT, Nairn AC, Arnold SE, Carlyle BC, Precioso F, Droit A. BERNN: Enhancing classification of Liquid Chromatography Mass Spectrometry data with batch effect removal neural networks. Nat Commun 2024;15:3777. [PMID: 38710683 PMCID: PMC11074280 DOI: 10.1038/s41467-024-48177-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 04/24/2024] [Indexed: 05/08/2024]  Open
20
Coorssen JR, Padula MP. Proteomics-The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience. Proteomes 2024;12:14. [PMID: 38651373 PMCID: PMC11036260 DOI: 10.3390/proteomes12020014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024]  Open
21
Xavier D, Lucas N, Williams SG, Koh JMS, Ashman K, Loudon C, Reddel R, Hains PG, Robinson PJ. Heat 'n Beat: A Universal High-Throughput End-to-End Proteomics Sample Processing Platform in under an Hour. Anal Chem 2024;96:4093-4102. [PMID: 38427620 DOI: 10.1021/acs.analchem.3c04708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
22
Yang Y, Mirzaei G. Performance analysis of data resampling on class imbalance and classification techniques on multi-omics data for cancer classification. PLoS One 2024;19:e0293607. [PMID: 38422094 PMCID: PMC10903850 DOI: 10.1371/journal.pone.0293607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/17/2023] [Indexed: 03/02/2024]  Open
23
Henke AN, Chilukuri S, Langan LM, Brooks BW. Reporting and reproducibility: Proteomics of fish models in environmental toxicology and ecotoxicology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024;912:168455. [PMID: 37979845 DOI: 10.1016/j.scitotenv.2023.168455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
24
Hartley B, Bassiouni W, Roczkowsky A, Fahlman R, Schulz R, Julien O. Data-Independent Acquisition Proteomics and N-Terminomics Methods Reveal Alterations in Mitochondrial Function and Metabolism in Ischemic-Reperfused Hearts. J Proteome Res 2024;23:844-856. [PMID: 38264990 PMCID: PMC10846531 DOI: 10.1021/acs.jproteome.3c00754] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 01/25/2024]
25
Zhong Q, Sun R, Aref AT, Noor Z, Anees A, Zhu Y, Lucas N, Poulos RC, Lyu M, Zhu T, Chen GB, Wang Y, Ding X, Rutishauser D, Rupp NJ, Rueschoff JH, Poyet C, Hermanns T, Fankhauser C, Rodríguez Martínez M, Shao W, Buljan M, Neumann JF, Beyer A, Hains PG, Reddel RR, Robinson PJ, Aebersold R, Guo T, Wild PJ. Proteomic-based stratification of intermediate-risk prostate cancer patients. Life Sci Alliance 2024;7:e202302146. [PMID: 38052461 PMCID: PMC10698198 DOI: 10.26508/lsa.202302146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023]  Open
26
Low RRJ, Fung KY, Dagley LF, Yousef J, Emery-Corbin SJ, Putoczki TL. Unbiased Quantitative Proteomics of Organoid Models of Pancreatic Cancer. Methods Mol Biol 2024;2823:77-93. [PMID: 39052215 DOI: 10.1007/978-1-0716-3922-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
27
Bichmann L, Gupta S, Röst H. Data-Independent Acquisition Peptidomics. Methods Mol Biol 2024;2758:77-88. [PMID: 38549009 DOI: 10.1007/978-1-0716-3646-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
28
Abid MSR, Qiu H, Checco JW. Label-Free Quantitation of Endogenous Peptides. Methods Mol Biol 2024;2758:125-150. [PMID: 38549012 PMCID: PMC11027169 DOI: 10.1007/978-1-0716-3646-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
29
Burnie J, Fernandes C, Chaphekar D, Wei D, Ahmed S, Persaud AT, Khader N, Cicala C, Arthos J, Tang VA, Guzzo C. Identification of CD38, CD97, and CD278 on the HIV surface using a novel flow virometry screening assay. Sci Rep 2023;13:23025. [PMID: 38155248 PMCID: PMC10754950 DOI: 10.1038/s41598-023-50365-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023]  Open
30
Kitata RB, Yang JC, Chen YJ. Advances in data-independent acquisition mass spectrometry towards comprehensive digital proteome landscape. MASS SPECTROMETRY REVIEWS 2023;42:2324-2348. [PMID: 35645145 DOI: 10.1002/mas.21781] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 06/15/2023]
31
Hay BN, Akinlaja MO, Baker TC, Houfani AA, Stacey RG, Foster LJ. Integration of data-independent acquisition (DIA) with co-fractionation mass spectrometry (CF-MS) to enhance interactome mapping capabilities. Proteomics 2023;23:e2200278. [PMID: 37144656 DOI: 10.1002/pmic.202200278] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 05/06/2023]
32
Gupta S, Sing JC, Röst HL. Achieving quantitative reproducibility in label-free multisite DIA experiments through multirun alignment. Commun Biol 2023;6:1101. [PMID: 37903988 PMCID: PMC10616189 DOI: 10.1038/s42003-023-05437-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 10/10/2023] [Indexed: 11/01/2023]  Open
33
Reilly L, Lara E, Ramos D, Li Z, Pantazis CB, Stadler J, Santiana M, Roberts J, Faghri F, Hao Y, Nalls MA, Narayan P, Liu Y, Singleton AB, Cookson MR, Ward ME, Qi YA. A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline. CELL REPORTS METHODS 2023;3:100593. [PMID: 37729920 PMCID: PMC10626189 DOI: 10.1016/j.crmeth.2023.100593] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 06/30/2023] [Accepted: 08/24/2023] [Indexed: 09/22/2023]
34
Searle BC, Chien A, Koller A, Hawke D, Herren AW, Kim Kim J, Lee KA, Leib RD, Nelson AJ, Patel P, Ren JM, Stemmer PM, Zhu Y, Neely BA, Patel B. A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development. Mol Cell Proteomics 2023;22:100639. [PMID: 37657519 PMCID: PMC10561125 DOI: 10.1016/j.mcpro.2023.100639] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]  Open
35
Buljan M, Banaei-Esfahani A, Blattmann P, Meier-Abt F, Shao W, Vitek O, Tang H, Aebersold R. A computational framework for the inference of protein complex remodeling from whole-proteome measurements. Nat Methods 2023;20:1523-1529. [PMID: 37749212 PMCID: PMC10555833 DOI: 10.1038/s41592-023-02011-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 08/16/2023] [Indexed: 09/27/2023]
36
Yu Y, Zhang N, Mai Y, Ren L, Chen Q, Cao Z, Chen Q, Liu Y, Hou W, Yang J, Hong H, Xu J, Tong W, Dong L, Shi L, Fang X, Zheng Y. Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method. Genome Biol 2023;24:201. [PMID: 37674217 PMCID: PMC10483871 DOI: 10.1186/s13059-023-03047-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/18/2023] [Indexed: 09/08/2023]  Open
37
Vanderaa C, Gatto L. Revisiting the Thorny Issue of Missing Values in Single-Cell Proteomics. J Proteome Res 2023;22:2775-2784. [PMID: 37530557 DOI: 10.1021/acs.jproteome.3c00227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
38
Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023;20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023]  Open
39
Midha MK, Kapil C, Maes M, Baxter DH, Morrone SR, Prokop TJ, Moritz RL. Vacuum Insulated Probe Heated Electrospray Ionization Source Enhances Microflow Rate Chromatography Signals in the Bruker timsTOF Mass Spectrometer. J Proteome Res 2023;22:2525-2537. [PMID: 37294184 PMCID: PMC11060334 DOI: 10.1021/acs.jproteome.3c00305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
40
Sun W, Lin Y, Huang Y, Chan J, Terrillon S, Rosenbaum AI, Contrepois K. Robust and High-Throughput Analytical Flow Proteomics Analysis of Cynomolgus Monkey and Human Matrices with Zeno SWATH Data Independent Acquisition. Mol Cell Proteomics 2023:100562. [PMID: 37142056 DOI: 10.1016/j.mcpro.2023.100562] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/17/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]  Open
41
Messner CB, Demichev V, Wang Z, Hartl J, Kustatscher G, Mülleder M, Ralser M. Mass spectrometry-based high-throughput proteomics and its role in biomedical studies and systems biology. Proteomics 2023;23:e2200013. [PMID: 36349817 DOI: 10.1002/pmic.202200013] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 11/11/2022]
42
Midha MK, Kapil C, Maes M, Baxter DH, Morrone SR, Prokop TJ, Moritz RL. Vacuum Insulated Probe Heated ElectroSpray Ionization source (VIP-HESI) enhances micro flow rate chromatography signals in the Bruker timsTOF mass spectrometer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528699. [PMID: 36824828 PMCID: PMC9949110 DOI: 10.1101/2023.02.15.528699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
43
Manuel JM, Guilloy N, Khatir I, Roucou X, Laurent B. Re-evaluating the impact of alternative RNA splicing on proteomic diversity. Front Genet 2023;14:1089053. [PMID: 36845399 PMCID: PMC9947481 DOI: 10.3389/fgene.2023.1089053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023]  Open
44
Sundararaman N, Bhat A, Venkatraman V, Binek A, Dwight Z, Ariyasinghe NR, Escopete S, Joung SY, Cheng S, Parker SJ, Fert-Bober J, Van Eyk JE. BIRCH: An Automated Workflow for Evaluation, Correction, and Visualization of Batch Effect in Bottom-Up Mass Spectrometry-Based Proteomics Data. J Proteome Res 2023;22:471-481. [PMID: 36695565 DOI: 10.1021/acs.jproteome.2c00671] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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He X, Liu X, Zuo F, Shi H, Jing J. Artificial intelligence-based multi-omics analysis fuels cancer precision medicine. Semin Cancer Biol 2023;88:187-200. [PMID: 36596352 DOI: 10.1016/j.semcancer.2022.12.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/16/2022] [Accepted: 12/29/2022] [Indexed: 01/02/2023]
46
Connolly EA, Grimison PS, Horvath LG, Robinson PJ, Reddel RR. Quantitative proteomic studies addressing unmet clinical needs in sarcoma. Front Oncol 2023;13:1126736. [PMID: 37197427 PMCID: PMC10183589 DOI: 10.3389/fonc.2023.1126736] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 03/31/2023] [Indexed: 05/19/2023]  Open
47
Vincent D, Bui A, Ezernieks V, Shahinfar S, Luke T, Ram D, Rigas N, Panozzo J, Rochfort S, Daetwyler H, Hayden M. A community resource to mass explore the wheat grain proteome and its application to the late-maturity alpha-amylase (LMA) problem. Gigascience 2022;12:giad084. [PMID: 37919977 PMCID: PMC10627334 DOI: 10.1093/gigascience/giad084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/02/2023] [Accepted: 09/19/2023] [Indexed: 11/04/2023]  Open
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Tear Proteome Revealed Association of S100A Family Proteins and Mesothelin with Thrombosis in Elderly Patients with Retinal Vein Occlusion. Int J Mol Sci 2022;23:ijms232314653. [PMID: 36498980 PMCID: PMC9736253 DOI: 10.3390/ijms232314653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/03/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]  Open
49
He B, Huang Z, Huang C, Nice EC. Clinical applications of plasma proteomics and peptidomics: Towards precision medicine. Proteomics Clin Appl 2022;16:e2100097. [PMID: 35490333 DOI: 10.1002/prca.202100097] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023]
50
Sabirov D, Ogurcov S, Baichurina I, Blatt N, Rizvanov A, Mukhamedshina Y. Molecular diagnostics in neurotrauma: Are there reliable biomarkers and effective methods for their detection? Front Mol Biosci 2022;9:1017916. [PMID: 36250009 PMCID: PMC9557129 DOI: 10.3389/fmolb.2022.1017916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/12/2022] [Indexed: 12/05/2022]  Open
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