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Brian Searle - Publications

Affiliations: 
2014-2018 Genome Sciences University of Washington, Seattle, Seattle, WA 
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37 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Heil LR, Damoc E, Arrey TN, Pashkova A, Denisov E, Petzoldt J, Peterson AC, Hsu C, Searle BC, Shulman N, Riffle M, Connolly B, MacLean BX, Remes PM, Senko MW, et al. Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data-Independent Acquisition. Journal of Proteome Research. PMID 37683181 DOI: 10.1021/acs.jproteome.3c00357  0.476
2023 Kirkpatrick J, Stemmer PM, Searle BC, Herring LE, Martin L, Midha MK, Phinney BS, Shan B, Palmblad M, Wang Y, Jagtap PD, Neely BA. 2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study. Journal of Biomolecular Techniques : Jbt. 34. PMID 37435391 DOI: 10.7171/3fc1f5fe.9b78d780  0.352
2023 Allen C, Meinl R, Paez JS, Searle BC, Just S, Pino LK, Fondrie WE. nf-encyclopedia: A Cloud-Ready Pipeline for Chromatogram Library Data-Independent Acquisition Proteomics Workflows. Journal of Proteome Research. PMID 37417926 DOI: 10.1021/acs.jproteome.2c00613  0.78
2023 Wilburn DB, Shannon AE, Spicer V, Richards AL, Yeung D, Swaney DL, Krokhin OV, Searle BC. Deep learning from harmonized peptide libraries enables retention time prediction of diverse post translational modifications. Biorxiv : the Preprint Server For Biology. PMID 37398395 DOI: 10.1101/2023.05.30.542978  0.348
2023 Heil LR, Damoc E, Arrey TN, Pashkova A, Denisov E, Petzoldt J, Peterson A, Hsu C, Searle BC, Shulman N, Riffle M, Connolly B, MacLean BX, Remes PM, Senko M, et al. Evaluating the performance of the Astral mass analyzer for quantitative proteomics using data independent acquisition. Biorxiv : the Preprint Server For Biology. PMID 37398334 DOI: 10.1101/2023.06.03.543570  0.476
2023 Phlairaharn T, Ye Z, Krismer E, Pedersen AK, Pietzner M, Olsen JV, Schoof EM, Searle BC. Optimizing Linear Ion-Trap Data-Independent Acquisition toward Single-Cell Proteomics. Analytical Chemistry. 95: 9881-9891. PMID 37338819 DOI: 10.1021/acs.analchem.3c00842  0.823
2023 Phlairaharn T, Ye Z, Krismer E, Pedersen AK, Pietzner M, Olsen JV, Schoof EM, Searle BC. Optimizing linear ion trap data independent acquisition towards single cell proteomics. Biorxiv : the Preprint Server For Biology. PMID 36865114 DOI: 10.1101/2023.02.21.529444  0.824
2023 Searle BC, Shannon AE, Wilburn DB. Scribe: Next Generation Library Searching for DDA Experiments. Journal of Proteome Research. PMID 36695531 DOI: 10.1021/acs.jproteome.2c00672  0.368
2023 Martinez TF, Lyons-Abbott S, Bookout AL, De Souza EV, Donaldson C, Vaughan JM, Lau C, Abramov A, Baquero AF, Baquero K, Friedrich D, Huard J, Davis R, Kim B, Koch T, ... ... Searle BC, et al. Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins. Cell Metabolism. 35: 166-183.e11. PMID 36599300 DOI: 10.1016/j.cmet.2022.12.004  0.696
2022 Phlairaharn T, Grégoire S, Woltereck LR, Petrosius V, Furtwängler B, Searle BC, Schoof EM. High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps. Journal of Proteome Research. 21: 2815-2826. PMID 36287219 DOI: 10.1021/acs.jproteome.2c00376  0.793
2022 Richards AL, Chen KH, Wilburn DB, Stevenson E, Polacco BJ, Searle BC, Swaney DL. Data-Independent Acquisition Protease-Multiplexing Enables Increased Proteome Sequence Coverage Across Multiple Fragmentation Modes. Journal of Proteome Research. PMID 35234472 DOI: 10.1021/acs.jproteome.1c00960  0.457
2021 Wilburn DB, Richards AL, Swaney DL, Searle BC. CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation. Journal of Proteome Research. PMID 33729787 DOI: 10.1021/acs.jproteome.0c00964  0.394
2020 Robinson AE, Binek A, Venkatraman V, Searle BC, Holewinski RJ, Rosenberger G, Parker SJ, Basisty N, Xie X, Lund PJ, Saxena G, Mato JM, Garcia BA, Schilling B, Lu SC, et al. Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease. Journal of Proteome Research. PMID 32966080 DOI: 10.1021/acs.jproteome.0c00685  0.46
2020 Pino LK, Just SC, MacCoss MJ, Searle BC. Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries. Molecular & Cellular Proteomics : McP. PMID 32312845 DOI: 10.1074/Mcp.P119.001913  0.808
2020 Searle BC, Swearingen KE, Barnes CA, Schmidt T, Gessulat S, Küster B, Wilhelm M. Generating high quality libraries for DIA MS with empirically corrected peptide predictions. Nature Communications. 11: 1548. PMID 32214105 DOI: 10.1038/S41467-020-15346-1  0.44
2020 Federation AJ, Nandakumar V, Searle BC, Stergachis A, Wang H, Pino LK, Merrihew G, Ting YS, Howard N, Kutyavin T, MacCoss MJ, Stamatoyannopoulos JA. Highly Parallel Quantification and Compartment Localization of Transcription Factors and Nuclear Proteins. Cell Reports. 30: 2463-2471.e5. PMID 32101728 DOI: 10.1016/J.Celrep.2020.01.096  0.731
2020 Pino LK, Searle BC, Yang HY, Hoofnagle AN, Noble WS, MacCoss MJ. Matrix-matched calibration curves for assessing analytical figures of merit in quantitative proteomics. Journal of Proteome Research. PMID 32037841 DOI: 10.1021/Acs.Jproteome.9B00666  0.793
2020 Jagtap P, Johnson J, Yang T, Fahrner M, Schilling O, Searle B, Griffin T. Exploring chromatogram library-based data-independent acquisition analysis using EncyclopeDIA within Galaxy framework. F1000research. 9. DOI: 10.7490/F1000Research.1118254.1  0.34
2019 Pino LK, Searle BC, Yang HY. Team COUNCIL OF RICKS submission for EUPA YPIC 2017. Eupa Open Proteomics. 22: 22-24. PMID 31890550 DOI: 10.1016/J.Euprot.2019.07.009  0.769
2019 Johnson R, Searle BC, Nunn BL, Gilmore JM, Phillips M, Amemiya CT, Heck M, MacCoss MJ. Assessing protein sequence database suitability using de novo sequencing. Molecular & Cellular Proteomics : McP. PMID 31732549 DOI: 10.1074/Mcp.Tir119.001752  0.799
2019 Searle BC, Lawrence RT, MacCoss MJ, Villén J. Thesaurus: quantifying phosphopeptide positional isomers. Nature Methods. 16: 703-706. PMID 31363206 DOI: 10.1038/S41592-019-0498-4  0.522
2018 Searle BC, Pino LK, Egertson JD, Ting YS, Lawrence RT, MacLean BX, Villén J, MacCoss MJ. Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry. Nature Communications. 9: 5128. PMID 30510204 DOI: 10.1038/S41467-018-07454-W  0.817
2018 Kim YJ, Sweet SM, Egertson JD, Sedgewick AJ, Woo S, Liao WL, Merrihew GE, Searle BC, Vaske C, Heaton R, MacCoss MJ, Hembrough T. Data-independent acquisition mass spectrometry to quantify protein levels in FFPE tumor biopsies for molecular diagnostics. Journal of Proteome Research. PMID 30481034 DOI: 10.1021/Acs.Jproteome.8B00699  0.777
2018 Pino LK, Searle BC, Huang E, Noble WS, Hoofnagle AN, MacCoss MJ. Calibration using a single-point external reference material harmonizes quantitative mass spectrometry proteomics data between platforms and laboratories. Analytical Chemistry. PMID 30350613 DOI: 10.1021/acs.analchem.8b04581  0.799
2018 Seitzer PM, Searle BC. Incorporating in-source fragment information improves metabolite identification accuracy in untargeted LC-MS datasets. Journal of Proteome Research. PMID 30295490 DOI: 10.1021/acs.jproteome.8b00601  0.318
2017 Ting YS, Egertson JD, Bollinger JG, Searle BC, Payne SH, Noble WS, MacCoss MJ. PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data. Nature Methods. PMID 28783153 DOI: 10.1038/Nmeth.4390  0.828
2017 Pino LK, Searle BC, Bollinger JG, Nunn B, MacLean B, MacCoss MJ. The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. Mass Spectrometry Reviews. PMID 28691345 DOI: 10.1002/Mas.21540  0.801
2016 Epstein JA, Blank PS, Searle BC, Catlin AD, Cologna SM, Olson MT, Backlund PS, Coorssen JR, Yergey AL. ProteinProcessor: A probabilistic analysis using mass accuracy and the MS spectrum. Proteomics. PMID 27546229 DOI: 10.1002/Pmic.201600137  0.49
2016 Lawrence RT, Searle BC, Llovet A, Villén J. Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry. Nature Methods. 13: 431-4. PMID 27018578 DOI: 10.1038/Nmeth.3811  0.397
2015 Cologna SM, Crutchfield CA, Searle BC, Blank PS, Toth CL, Ely AM, Picache JA, Backlund PS, Wassif CA, Porter FD, Yergey AL. An Efficient Approach to Evaluate Reporter Ion Behavior from MALDI-MS/MS Data for Quantification Studies Using Isobaric Tags. Journal of Proteome Research. 14: 4169-78. PMID 26288259 DOI: 10.1021/Acs.Jproteome.5B00254  0.507
2015 Searle BC, Egertson JD, Bollinger JG, Stergachis AB, MacCoss MJ. Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments. Molecular & Cellular Proteomics : McP. 14: 2331-40. PMID 26100116 DOI: 10.1074/Mcp.M115.051300  0.784
2012 Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, et al. The mzIdentML data standard for mass spectrometry-based proteomics results. Molecular & Cellular Proteomics : McP. 11: M111.014381. PMID 22375074 DOI: 10.1074/Mcp.M111.014381  0.362
2011 Eng JK, Searle BC, Clauser KR, Tabb DL. A face in the crowd: recognizing peptides through database search. Molecular & Cellular Proteomics : McP. 10: R111.009522. PMID 21876205 DOI: 10.1074/Mcp.R111.009522  0.504
2010 Searle BC. Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies. Proteomics. 10: 1265-9. PMID 20077414 DOI: 10.1002/pmic.200900437  0.349
2008 Searle BC, Turner M, Nesvizhskii AI. Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies. Journal of Proteome Research. 7: 245-53. PMID 18173222 DOI: 10.1021/Pr070540W  0.402
2005 Searle BC, Dasari S, Wilmarth PA, Turner M, Reddy AP, David LL, Nagalla SR. Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm. Journal of Proteome Research. 4: 546-54. PMID 15822933 DOI: 10.1021/pr049781j  0.438
2004 Searle BC, Dasari S, Turner M, Reddy AP, Choi D, Wilmarth PA, McCormack AL, David LL, Nagalla SR. High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results. Analytical Chemistry. 76: 2220-30. PMID 15080731 DOI: 10.1021/ac035258x  0.391
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