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For: Muntel J, Boswell SA, Tang S, Ahmed S, Wapinski I, Foley G, Steen H, Springer M. Abundance-based classifier for the prediction of mass spectrometric peptide detectability upon enrichment (PPA). Mol Cell Proteomics 2014;14:430-40. [PMID: 25473088 DOI: 10.1074/mcp.m114.044321] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
Number Cited by Other Article(s)
1
Abdul-Khalek N, Picciani M, Shouman O, Wimmer R, Overgaard MT, Wilhelm M, Gregersen Echers S. To Fly, or Not to Fly, That Is the Question: A Deep Learning Model for Peptide Detectability Prediction in Mass Spectrometry. J Proteome Res 2025. [PMID: 40344201 DOI: 10.1021/acs.jproteome.4c00973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2025]
2
Wang Z, Liu PK, Li L. A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics. ACS MEASUREMENT SCIENCE AU 2024;4:315-337. [PMID: 39184361 PMCID: PMC11342459 DOI: 10.1021/acsmeasuresciau.4c00007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 08/27/2024]
3
Kalhor M, Lapin J, Picciani M, Wilhelm M. Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification. Mol Cell Proteomics 2024;23:100798. [PMID: 38871251 PMCID: PMC11269915 DOI: 10.1016/j.mcpro.2024.100798] [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: 05/26/2024] [Accepted: 06/09/2024] [Indexed: 06/15/2024]  Open
4
Abdul-Khalek N, Wimmer R, Overgaard MT, Gregersen Echers S. Insight on physicochemical properties governing peptide MS1 response in HPLC-ESI-MS/MS: A deep learning approach. Comput Struct Biotechnol J 2023;21:3715-3727. [PMID: 37560124 PMCID: PMC10407266 DOI: 10.1016/j.csbj.2023.07.027] [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: 03/06/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023]  Open
5
Rusilowicz M, Newman DW, Creamer DR, Johnson J, Adair K, Harman VM, Grant CM, Beynon RJ, Hubbard SJ. AlacatDesigner─Computational Design of Peptide Concatamers for Protein Quantitation. J Proteome Res 2023;22:594-604. [PMID: 36688735 PMCID: PMC9903321 DOI: 10.1021/acs.jproteome.2c00608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
6
Dincer AB, Lu Y, Schweppe DK, Oh S, Noble WS. Reducing Peptide Sequence Bias in Quantitative Mass Spectrometry Data with Machine Learning. J Proteome Res 2022;21:1771-1782. [PMID: 35696663 DOI: 10.1021/acs.jproteome.2c00211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
7
WEN H, ZHU J, ZHANG B. [Recent advances in microchip liquid chromatography]. Se Pu 2021;39:357-367. [PMID: 34227755 PMCID: PMC9404124 DOI: 10.3724/sp.j.1123.2020.07031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Indexed: 11/25/2022]  Open
8
Wilburn DB, Richards AL, Swaney DL, Searle BC. CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation. J Proteome Res 2021;20:1951-1965. [PMID: 33729787 DOI: 10.1021/acs.jproteome.0c00964] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
9
Waas M, Littrell J, Gundry RL. CIRFESS: An Interactive Resource for Querying the Set of Theoretically Detectable Peptides for Cell Surface and Extracellular Enrichment Proteomic Studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020;31:1389-1397. [PMID: 32212654 PMCID: PMC8116119 DOI: 10.1021/jasms.0c00021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
10
Pino LK, Searle BC, Bollinger JG, Nunn B, MacLean B, MacCoss MJ. The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. MASS SPECTROMETRY REVIEWS 2020;39:229-244. [PMID: 28691345 PMCID: PMC5799042 DOI: 10.1002/mas.21540] [Citation(s) in RCA: 507] [Impact Index Per Article: 101.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 06/01/2017] [Indexed: 05/03/2023]
11
Gao Z, Chang C, Yang J, Zhu Y, Fu Y. AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility. Anal Chem 2019;91:8705-8711. [DOI: 10.1021/acs.analchem.9b02520] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
12
Pappireddi N, Martin L, Wühr M. A Review on Quantitative Multiplexed Proteomics. Chembiochem 2019;20:1210-1224. [PMID: 30609196 PMCID: PMC6520187 DOI: 10.1002/cbic.201800650] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/27/2018] [Indexed: 12/11/2022]
13
Kecskemeti A, Gaspar A. Particle-based liquid chromatographic separations in microfluidic devices - A review. Anal Chim Acta 2018;1021:1-19. [DOI: 10.1016/j.aca.2018.01.064] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/18/2018] [Accepted: 01/21/2018] [Indexed: 01/06/2023]
14
Haghighi F, Talebpour Z, Nezhad AS. Towards fully integrated liquid chromatography on a chip: Evolution and evaluation. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.05.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
15
Jonckheere W, Dermauw W, Khalighi M, Pavlidi N, Reubens W, Baggerman G, Tirry L, Menschaert G, Kant MR, Vanholme B, Van Leeuwen T. A Gene Family Coding for Salivary Proteins (SHOT) of the Polyphagous Spider Mite Tetranychus urticae Exhibits Fast Host-Dependent Transcriptional Plasticity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018;31:112-124. [PMID: 29094648 DOI: 10.1094/mpmi-06-17-0139-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
16
Abelin JG, Keskin DB, Sarkizova S, Hartigan CR, Zhang W, Sidney J, Stevens J, Lane W, Zhang GL, Eisenhaure TM, Clauser KR, Hacohen N, Rooney MS, Carr SA, Wu CJ. Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction. Immunity 2017;46:315-326. [PMID: 28228285 DOI: 10.1016/j.immuni.2017.02.007] [Citation(s) in RCA: 451] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 11/29/2016] [Accepted: 12/29/2016] [Indexed: 12/11/2022]
17
Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer. Sci Data 2017;4:170091. [PMID: 28722704 PMCID: PMC5516542 DOI: 10.1038/sdata.2017.91] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 06/01/2017] [Indexed: 02/06/2023]  Open
18
Jarnuczak AF, Lee DCH, Lawless C, Holman SW, Eyers CE, Hubbard SJ. Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics. J Proteome Res 2016;15:2945-59. [PMID: 27454336 DOI: 10.1021/acs.jproteome.6b00048] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
19
Singh SA, Aikawa E, Aikawa M. Current Trends and Future Perspectives of State-of-the-Art Proteomics Technologies Applied to Cardiovascular Disease Research. Circ J 2016;80:1674-83. [PMID: 27430298 DOI: 10.1253/circj.cj-16-0499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
20
Hoofnagle AN, Whiteaker JR, Carr SA, Kuhn E, Liu T, Massoni SA, Thomas SN, Townsend RR, Zimmerman LJ, Boja E, Chen J, Crimmins DL, Davies SR, Gao Y, Hiltke TR, Ketchum KA, Kinsinger CR, Mesri M, Meyer MR, Qian WJ, Schoenherr RM, Scott MG, Shi T, Whiteley GR, Wrobel JA, Wu C, Ackermann BL, Aebersold R, Barnidge DR, Bunk DM, Clarke N, Fishman JB, Grant RP, Kusebauch U, Kushnir MM, Lowenthal MS, Moritz RL, Neubert H, Patterson SD, Rockwood AL, Rogers J, Singh RJ, Van Eyk JE, Wong SH, Zhang S, Chan DW, Chen X, Ellis MJ, Liebler DC, Rodland KD, Rodriguez H, Smith RD, Zhang Z, Zhang H, Paulovich AG. Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays. Clin Chem 2016;62:48-69. [PMID: 26719571 DOI: 10.1373/clinchem.2015.250563] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
21
Searle BC, Egertson JD, Bollinger JG, Stergachis AB, MacCoss MJ. Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments. Mol Cell Proteomics 2015;14:2331-40. [PMID: 26100116 DOI: 10.1074/mcp.m115.051300] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Indexed: 11/06/2022]  Open
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