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For: McGurk KA, Dagliati A, Chiasserini D, Lee D, Plant D, Baricevic-Jones I, Kelsall J, Eineman R, Reed R, Geary B, Unwin RD, Nicolaou A, Keavney BD, Barton A, Whetton AD, Geifman N. The use of missing values in proteomic data-independent acquisition mass spectrometry to enable disease activity discrimination. Bioinformatics 2020;36:2217-2223. [PMID: 31790148 PMCID: PMC7141869 DOI: 10.1093/bioinformatics/btz898] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/14/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022]  Open
Number Cited by Other Article(s)
1
Dube CT, Gilbert HTJ, Rabbitte N, Baird P, Patel S, Herrera JA, Baricevic-Jones I, Unwin RD, Chan D, Gnanalingham K, Hoyland JA, Richardson SM. Proteomic profiling of human plasma and intervertebral disc tissue reveals matrisomal, but not plasma, biomarkers of disc degeneration. Arthritis Res Ther 2025;27:28. [PMID: 39930483 PMCID: PMC11809052 DOI: 10.1186/s13075-025-03489-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Accepted: 01/26/2025] [Indexed: 02/14/2025]  Open
2
Mondelo-Macía P, García-González J, León-Mateos L, Abalo A, Bravo S, Chantada Vazquez MDP, Muinelo-Romay L, López-López R, Díaz-Peña R, Dávila-Ibáñez AB. Identification of a Proteomic Signature for Predicting Immunotherapy Response in Patients With Metastatic Non-Small Cell Lung Cancer. Mol Cell Proteomics 2024;23:100834. [PMID: 39216661 PMCID: PMC11474190 DOI: 10.1016/j.mcpro.2024.100834] [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: 05/26/2023] [Revised: 08/17/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]  Open
3
Nygren D, Torisson G, Happonen L, Mellhammar L, Linder A, Elf J, Yan H, Welinder C, Holm K. Proteomic Characterization of Plasma in Lemierre's Syndrome. Thromb Haemost 2024;124:432-440. [PMID: 37857346 PMCID: PMC11038868 DOI: 10.1055/a-2195-3927] [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: 05/05/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
4
Burns AR, Wiedrick J, Feryn A, Maes M, Midha MK, Baxter DH, Morrone SR, Prokop TJ, Kapil C, Hoopmann MR, Kusebauch U, Deutsch EW, Rappaport N, Watanabe K, Moritz RL, Miller RA, Lapidus JA, Orwoll ES. Proteomic changes induced by longevity-promoting interventions in mice. GeroScience 2024;46:1543-1560. [PMID: 37653270 PMCID: PMC10828338 DOI: 10.1007/s11357-023-00917-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/20/2023] [Indexed: 09/02/2023]  Open
5
Turner N, Abeysinghe P, Flay H, Meier S, Sadowski P, Mitchell MD. SWATH-MS Analysis of Blood Plasma and Circulating Small Extracellular Vesicles Enables Detection of Putative Protein Biomarkers of Fertility in Young and Aged Dairy Cows. J Proteome Res 2023;22:3580-3595. [PMID: 37830897 DOI: 10.1021/acs.jproteome.3c00406] [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: 10/14/2023]
6
Wang J, Yu W, D'Anna R, Przybyla A, Wilson M, Sung M, Bullen J, Hurt E, D'Angelo G, Sidders B, Lai Z, Zhong W. Pan-Cancer Proteomics Analysis to Identify Tumor-Enriched and Highly Expressed Cell Surface Antigens as Potential Targets for Cancer Therapeutics. Mol Cell Proteomics 2023;22:100626. [PMID: 37517589 PMCID: PMC10494184 DOI: 10.1016/j.mcpro.2023.100626] [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: 01/23/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023]  Open
7
Ramírez Medina CR, Ali I, Baricevic-Jones I, Odudu A, Saleem MA, Whetton AD, Kalra PA, Geifman N. Proteomic signature associated with chronic kidney disease (CKD) progression identified by data-independent acquisition mass spectrometry. Clin Proteomics 2023;20:19. [PMID: 37076799 PMCID: PMC10116780 DOI: 10.1186/s12014-023-09405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/14/2023] [Indexed: 04/21/2023]  Open
8
Wolski WE, Nanni P, Grossmann J, d'Errico M, Schlapbach R, Panse C. prolfqua: A Comprehensive R-Package for Proteomics Differential Expression Analysis. J Proteome Res 2023;22:1092-1104. [PMID: 36939687 PMCID: PMC10088014 DOI: 10.1021/acs.jproteome.2c00441] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
9
A Novel Blood Proteomic Signature for Prostate Cancer. Cancers (Basel) 2023;15:cancers15041051. [PMID: 36831393 PMCID: PMC9954127 DOI: 10.3390/cancers15041051] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023]  Open
10
Machipisa T, Chishala C, Shaboodien G, Zühlke LJ, Muhamed B, Pandie S, de Vries J, Laing N, Joachim A, Daniels R, Ntsekhe M, Hugo-Hamman CT, Gitura B, Ogendo S, Lwabi P, Okello E, Damasceno A, Novela C, Mocumbi AO, Madeira G, Musuku J, Mtaja A, ElSayed A, Alhassan HH, Bode-Thomas F, Yilgwan C, Amusa G, Nkereuwem E, Mulder N, Ramesar R, Lesosky M, Cordell HJ, Chong M, Keavney B, Paré G, Engel ME. Rationale, Design, and the Baseline Characteristics of the RHDGen (The Genetics of Rheumatic Heart Disease) Network Study†. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023;16:e003641. [PMID: 36548480 PMCID: PMC9946164 DOI: 10.1161/circgen.121.003641] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 08/30/2022] [Indexed: 12/24/2022]
11
Kong W, Hui HWH, Peng H, Goh WWB. Dealing with missing values in proteomics data. Proteomics 2022;22:e2200092. [PMID: 36349819 DOI: 10.1002/pmic.202200092] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/15/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022]
12
Fröhlich K, Brombacher E, Fahrner M, Vogele D, Kook L, Pinter N, Bronsert P, Timme-Bronsert S, Schmidt A, Bärenfaller K, Kreutz C, Schilling O. Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity. Nat Commun 2022;13:2622. [PMID: 35551187 PMCID: PMC9098472 DOI: 10.1038/s41467-022-30094-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/14/2022] [Indexed: 12/25/2022]  Open
13
Iqbal Z, Fachim HA, Gibson JM, Baricevic-Jones I, Campbell AE, Geary B, Donn RP, Hamarashid D, Syed A, Whetton AD, Soran H, Heald AH. Changes in the Proteome Profile of People Achieving Remission of Type 2 Diabetes after Bariatric Surgery. J Clin Med 2021;10:3659. [PMID: 34441954 PMCID: PMC8396849 DOI: 10.3390/jcm10163659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023]  Open
14
Egert J, Brombacher E, Warscheid B, Kreutz C. DIMA: Data-Driven Selection of an Imputation Algorithm. J Proteome Res 2021;20:3489-3496. [PMID: 34062065 DOI: 10.1021/acs.jproteome.1c00119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
15
Quiroz-Baez R, Hernández-Ortega K, Martínez-Martínez E. Insights Into the Proteomic Profiling of Extracellular Vesicles for the Identification of Early Biomarkers of Neurodegeneration. Front Neurol 2020;11:580030. [PMID: 33362690 PMCID: PMC7759525 DOI: 10.3389/fneur.2020.580030] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022]  Open
16
Weghorst F, Mirzakhanyan Y, Samimi K, Dhillon M, Barzik M, Cunningham LL, Gershon PD, Cramer KS. Caspase-3 Cleaves Extracellular Vesicle Proteins During Auditory Brainstem Development. Front Cell Neurosci 2020;14:573345. [PMID: 33281555 PMCID: PMC7689216 DOI: 10.3389/fncel.2020.573345] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022]  Open
17
Cai X, Ge W, Yi X, Sun R, Zhu J, Lu C, Sun P, Zhu T, Ruan G, Yuan C, Liang S, Lyu M, Huang S, Zhu Y, Guo T. PulseDIA: Data-Independent Acquisition Mass Spectrometry Using Multi-Injection Pulsed Gas-Phase Fractionation. J Proteome Res 2020;20:279-288. [PMID: 32975123 DOI: 10.1021/acs.jproteome.0c00381] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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