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For: Lin A, Howbert JJ, Noble WS. Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data. J Proteome Res 2018;17:3644-3656. [PMID: 30221945 DOI: 10.1021/acs.jproteome.8b00206] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Number Cited by Other Article(s)
1
Madej D, Lam H. PyViscount: Validating False Discovery Rate Estimation Methods via Random Search Space Partition. J Proteome Res 2025;24:1118-1134. [PMID: 39905949 PMCID: PMC11894659 DOI: 10.1021/acs.jproteome.4c00743] [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: 08/28/2024] [Revised: 01/20/2025] [Accepted: 01/28/2025] [Indexed: 02/06/2025]
2
Deshpande AS, Lin A, O'Bryon I, Aufrecht JA, Merkley ED. Emerging protein sequencing technologies: proteomics without mass spectrometry? Expert Rev Proteomics 2025;22:89-106. [PMID: 40105028 DOI: 10.1080/14789450.2025.2476979] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Revised: 02/12/2025] [Accepted: 03/03/2025] [Indexed: 03/20/2025]
3
Chu F, Lin A. Detecting Human Contaminant Genetically Variant Peptides in Nonhuman Samples. J Proteome Res 2025;24:579-588. [PMID: 39705712 DOI: 10.1021/acs.jproteome.4c00718] [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: 12/22/2024]
4
Lin A, See D, Fondrie WE, Keich U, Noble WS. Target-decoy false discovery rate estimation using Crema. Proteomics 2024;24:e2300084. [PMID: 38380501 DOI: 10.1002/pmic.202300084] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 01/06/2024] [Accepted: 01/16/2024] [Indexed: 02/22/2024]
5
Bhimani K, Peresadina A, Vozniuk D, Kertész-Farkas A. Exact p-value calculation for XCorr scoring of high-resolution MS/MS data. Proteomics 2024;24:e2300145. [PMID: 37726251 DOI: 10.1002/pmic.202300145] [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: 03/18/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023]
6
Kertesz-Farkas A, Nii Adoquaye Acquaye FL, Bhimani K, Eng JK, Fondrie WE, Grant C, Hoopmann MR, Lin A, Lu YY, Moritz RL, MacCoss MJ, Noble WS. The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data. J Proteome Res 2023;22:561-569. [PMID: 36598107 DOI: 10.1021/acs.jproteome.2c00615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
7
Lin A, Deatherage Kaiser BL, Hutchison JR, Bilmes JA, Noble WS. MS1Connect: a mass spectrometry run similarity measure. Bioinformatics 2023;39:7005198. [PMID: 36702456 PMCID: PMC9913042 DOI: 10.1093/bioinformatics/btad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 01/05/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023]  Open
8
Lin A, Short T, Noble WS, Keich U. Improving Peptide-Level Mass Spectrometry Analysis via Double Competition. J Proteome Res 2022;21:2412-2420. [PMID: 36166314 PMCID: PMC10108709 DOI: 10.1021/acs.jproteome.2c00282] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
9
Kudriavtseva P, Kashkinov M, Kertész-Farkas A. Deep Convolutional Neural Networks Help Scoring Tandem Mass Spectrometry Data in Database-Searching Approaches. J Proteome Res 2021;20:4708-4717. [PMID: 34449232 DOI: 10.1021/acs.jproteome.1c00315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
10
Lin A, Plubell DL, Keich U, Noble WS. Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant. J Proteome Res 2021;20:4153-4164. [PMID: 34236864 PMCID: PMC8489664 DOI: 10.1021/acs.jproteome.1c00483] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
11
Fondrie W, Noble WS. mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection. J Proteome Res 2021;20:1966-1971. [PMID: 33596079 PMCID: PMC8022319 DOI: 10.1021/acs.jproteome.0c01010] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Indexed: 12/23/2022]
12
Development of an MS Workflow Based on Combining Database Search Engines for Accurate Protein Identification and Its Validation to Identify the Serum Proteomic Profile in Female Stress Urinary Incontinence. BIOMED RESEARCH INTERNATIONAL 2020. [DOI: 10.1155/2020/8740468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
13
Sulimov P, Voronkova A, Kertész-Farkas A. Annotation of tandem mass spectrometry data using stochastic neural networks in shotgun proteomics. Bioinformatics 2020;36:3781-3787. [PMID: 32207518 DOI: 10.1093/bioinformatics/btaa206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 11/12/2022]  Open
14
Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis. Int J Mol Sci 2020;21:ijms21082873. [PMID: 32326049 PMCID: PMC7216093 DOI: 10.3390/ijms21082873] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 01/15/2023]  Open
15
Sulimov P, Kertész-Farkas A. Tailor: A Nonparametric and Rapid Score Calibration Method for Database Search-Based Peptide Identification in Shotgun Proteomics. J Proteome Res 2020;19:1481-1490. [DOI: 10.1021/acs.jproteome.9b00736] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
16
Fondrie WE, Noble WS. Machine Learning Strategy That Leverages Large Data sets to Boost Statistical Power in Small-Scale Experiments. J Proteome Res 2020;19:1267-1274. [PMID: 32009418 PMCID: PMC8455073 DOI: 10.1021/acs.jproteome.9b00780] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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