Publications

1. Moore MG, Garlapally V, Brusach KB, Akshintala VS, Babcock L, Gurria J, Hornung L, Saad M, Sheridan R, Trout A, Zhang L, Cruz-Monserrate Z, Searle BC, Abu-El-Haija M. Urine Proteomics Identifies Biomarkers for Diagnosis and Fibrosis Severity in Pediatric Chronic Pancreatitis. Clin Transl Gastroenterol. 2026 Mar 1; 17 (3):e00981 Epub 2026 Mar 01
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2. Rajczewski AT, Mehta S, Wagner R, Gabriel W, Johnson J, Do K, Vintila S, Wilhelm M, Kleiner M, Searle BC, Griffin TJ, Jagtap PD. Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset. J Proteomics. 2026 Jan 6; 322:105549 Epub 2025 Oct 21
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3. Brusach KB, Shannon AE, Joyce AW, Quimby JM, Searle BC. Harmonized Peptide Libraries Enable Practical Biofluid Selection for Developing Biomarker Assays. Mol Cell Proteomics. 2025 Dec; 24 (12):101086 Epub 2025 Oct 12
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4. Lautenbacher L, Yang KL, Kockmann T, Panse C, Gabriel W, Bold D, Kahl E, Chambers M, MacLean BX, Li K, Yu F, Searle BC, Wilburn DB, Shahneh MRZ, Hong Y, Tang H, Wang M, Gabriels R, Bouwmeester R, Devreese R, Angelis J, Sabidó E, Schmidt TK, Nesvizhskii AI, Wilhelm M. Koina: Democratizing machine learning for proteomics research. Nat Commun. 2025 Nov 11; 16(1):9933.
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5. Wang Y, Ma A, Song NJ, Shannon AE, Amankwah YS, Chen X, Wu W, Wang Z, Saadey AA, Yousif A, Ghosh G, Mandula JK, Velegraki M, Xiao T, Wen H, Huang SC, Wang R, Beusch CM, Dawood AS, Gordon DE, Abdel-Hakeem MS, Ghoneim HE, Xin G, Searle BC, Li Z. Proteotoxic stress response drives T cell exhaustion and immune evasion. Nature. 2025 Nov; 647(8091):1025-1035. Epub 2025 Oct 01.
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6. Phlairaharn T, Shannon AE, Zeng X, Truong DJ, Schoof EM, Ye Z, Searle BC. Improving Proteomic Dynamic Range with Multiple Accumulation Precursor Mass Spectrometry. J Proteome Res. 2025 Oct 3; 24 (10):5116-5126 Epub 2025 Sept 12
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7. Gan YJ, Hazel JM, Searle BC, Shafaat HS. Selective isotope labeling probes the chemical capacity and reaction mechanism of a heterobimetallic Mn/Fe protein. J Inorg Biochem. 2025 Sep; 270:112933 Epub 2025 Apr 23
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8. Meyer ACS, McIlvin MR, Lopez P, Searle BC, Saito MA. Proteomic profiling of zinc homeostasis mechanisms in Pseudomonas aeruginosa through data-dependent and data-independent acquisition mass spectrometry. Metallomics. 2025 Aug 5; 17 (8)
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9. Li W, Pergande MR, Serna-Perez F, Patel V, Crutchfield CA, Searle BC, Picache JA, Farhat NM, Wassif CA, Backlund PS, Bianconi S, Pacak K, Freel BA, Francis KR, Porter FD, Cologna SM. Altered Cerebrospinal Fluid Proteins in Smith-Lemli-Opitz Syndrome. J Proteome Res. 2025 Aug 1; 24 (8):4154-4165 Epub 2025 July 09
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10. Mars Brisbin M, McIlvin MR, Wilburn DB, Saunders JK, Cohen NR, Bhatia M, Kujawinski E, Searle BC, Saito MA. Validation and Community Sharing of Ocean Spectral Libraries Generated by Machine Learning for Data Independent Acquisition Ocean Metaproteomic Analyses. Proteomics. 2025 Jun 11; e13971 Epub 2025 June 11
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11. Rajczewski AT, Blakeley-Ruiz JA, Meyer A, Vintila S, McIlvin MR, Van Den Bossche T, Searle BC, Griffin TJ, Saito MA, Kleiner M, Jagtap PD. Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome. Proteomics. 2025 May; 25 (9-10):e202400187 Epub 2025 Apr 10
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12. Shannon AE, Teodorescu RN, Song NJ, Heil LR, Jacob CC, Remes PM, Li Z, Rubinstein MP, Searle BC. Rapid assay development for low input targeted proteomics using a versatile linear ion trap. Nat Commun. 2025 Apr 23; 16 (1):3794
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13. Ghosh G, Shannon AE, Searle BC. Data acquisition approaches for single cell proteomics. Proteomics. 2025 Jan; 25 (1-2):e2400022 Epub 2024 Aug 01
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14. Searle BC. Characterizing protein-protein interactions with thermal proteome profiling. Curr Opin Struct Biol. 2024 Dec; 89:102946 Epub 2024 Oct 30
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15. Saito MA, Saunders JK, McIlvin MR, Bertrand EM, Breier JA, Brisbin MM, Colston S, Compton JR, Griffin T, Hervey J, Hettich RL, Jagtap P, Janech M, Johnson R, Keil R, Kleikamp H, Leary D, McCain JSP, Moore E, Mehta S, Moran DM, Neibauer J, Neely B, Jakuba MV, Johnson J, Duffy M, Herndl GJ, Giannone R, Mueller R, Nunn BL, Pabst M, Peters S, Rajczewski A, Rowland E, Searle BC, Bossche TVD, Vora GJ, Waldbauer J, Zheng H, Zhao Z. Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures Biogeosciences. 2024; 21(21):4889-4908.
    
16. Akshintala VS, Moore MG, Cruz-Monserrate Z, Nathan JD, Searle BC, Abu-El-Haija M. Urine Proteomics Profiling Identifies Novel Acute Pancreatitis Diagnostic Biomarkers in a Pediatric Population. Gastroenterology. 2024 Oct; 167 (5):1019-1021.e2 Epub 2024 May 24
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17. Shannon AE, Boos CE, Searle BC, Hummon AB. Gas-Phase Fractionation Data-Independent Acquisition Analysis of 3D Cocultured Spheroid Tumor Model Reveals Altered Translational Processes and Signaling Using Proteomics. J Proteome Res. 2024 Aug 2; 23 (8):3188-3199 Epub 2024 Feb 27
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18. Searle BC. Nanopore Protein Sequencing Achieves Significant New Milestones. Clin Chem. 2024 Aug 1; 70 (8):1006-1008
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19. Joyce AW, Searle BC. Computational approaches to identify sites of phosphorylation. Proteomics. 2024 Apr; 24 (8):e2300088 Epub 2023 Dec 24
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20. 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, Stewart HI, Hock C, Makarov AA, Hermanson D, Zabrouskov V, Wu CC, MacCoss MJ. Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data-Independent Acquisition. J Proteome Res. 2023 Oct 6; 22 (10):3290-3300 Epub 2023 Sept 08
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21. 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 Oct; 22 (10):100639 Epub 2023 Aug 30
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22. 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. J Proteome Res. 2023 Aug 4; 22 (8):2743-2749 Epub 2023 July 07
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23. 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. Anal Chem. 2023 Jul 4; 95 (26):9881-9891 Epub 2023 June 20
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24. 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. J Biomol Tech. 2023 Jul 1; 34 (2) Epub 2023 June 02
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25. Li W, Pergande MR, Crutchfield CA, Searle BC, Backlund PS, Picache JA, Burkert K, Yanjanin-Farhat NM, Blank PS, Toth CL, Wassif CA, Porter FD, Cologna SM. A differential proteomics study of cerebrospinal fluid from individuals with Niemann-Pick disease, Type C1. Proteomics. 2023 Jun; 23 (11):e2200378 Epub 2023 Jan 26
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26. Merrihew GE, Park J, Plubell D, Searle BC, Keene CD, Larson EB, Bateman R, Perrin RJ, Chhatwal JP, Farlow MR, McLean CA, Ghetti B, Newell KL, Frosch MP, Montine TJ, MacCoss MJ. A peptide-centric quantitative proteomics dataset for the phenotypic assessment of Alzheimer's disease. Sci Data. 2023 Apr 14; 10 (1):206
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27. Searle BC, Shannon AE, Wilburn DB. Scribe: Next Generation Library Searching for DDA Experiments. J Proteome Res. 2023 Feb 3; 22 (2):482-490 Epub 2023 Jan 25
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28. 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, Mercer AJ, Misquith A, Murray SA, Perry S, Pino LK, Sanford C, Simon A, Zhang Y, Zipp G, Bizarro CV, Shokhirev MN, Whittle AJ, Searle BC, MacCoss MJ, Saghatelian A, Barnes CA. Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins. Cell Metab. 2023 Jan 3; 35 (1):166-183.e11
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29. Phlairaharn T, Gregoire S, Woltereck LR, Petrosius V, Furtwangler B, Searle BC, Schoof EM. High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps. J Proteome Res. 2022 Nov 4; 21 (11):2815-2826 Epub 2022 Oct 26
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30. 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. J Proteome Res. 2022 Apr 1; 21 (4):1124-1136 Epub 2022 Mar 02
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31. Wilburn DB, Kunkel CL, Feldhoff RC, Feldhoff PW, Searle BC. Recurrent Co-Option and Recombination of Cytokine and Three Finger Proteins in Multiple Reproductive Tissues Throughout Salamander Evolution. Front Cell Dev Biol. 2022; 10:828947 Epub 2022 Feb 23
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32. McEllin B, Searle BC, DePledge L, Sun G, Cobbs C, Karimi M. Detection of Human Papillomavirus Integration in Brain Metastases from Oropharyngeal Tumors by Targeted Sequencing. Viruses. 2021 Aug 3; 13 (8) Epub 2021 Aug 03
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33. Wilburn DB, Richards AL, Swaney DL, Searle BC. CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation. J Proteome Res. 2021 Apr 2; 20 (4):1951-1965 Epub 2021 Mar 17
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34. 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, Van Eyk JE. Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease. J Proteome Res. 2020 Oct 2; 19 (10):4163-4178 Epub 2020 Sept 23
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35. Searle BC, Yergey AL. An efficient solution for resolving iTRAQ and TMT channel cross-talk. J Mass Spectrom. 2020 Aug; 55 (8):e4354 Epub 2019 Apr 29
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36. Pino LK, Just SC, MacCoss MJ, Searle BC. Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries. Mol Cell Proteomics. 2020 Jul; 19 (7):1088-1103 Epub 2020 Apr 20
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37. Pino LK, Searle BC, Bollinger JG, Nunn B, MacLean B, MacCoss MJ. The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. Mass Spectrom Rev. 2020 May; 39 (3):229-244 Epub 2017 July 09
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38. Mische SM, Fisher NC, Meyn SM, Sol-Church K, Hegstad-Davies RL, Weis-Garcia F, Adams M, Ashton JM, Delventhal KM, Dragon JA, Holmes L, Jagtap P, Kubow KE, Mason CE, Palmblad M, Searle BC, Turck CW, Knudtson KL. A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups. J Biomol Tech. 2020 Apr; 31 (1):11-26
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39. Searle BC, Swearingen KE, Barnes CA, Schmidt T, Gessulat S, Kuster B, Wilhelm M. Generating high quality libraries for DIA MS with empirically corrected peptide predictions. Nat Commun. 2020 Mar 25; 11 (1):1548
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40. 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. J Proteome Res. 2020 Mar 6; 19 (3):1147-1153 Epub 2020 Feb 24
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41. 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 Rep. 2020 Feb 25; 30 (8):2463-2471.e5
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42. Johnson RS, Searle BC, Nunn BL, Gilmore JM, Phillips M, Amemiya CT, Heck M, MacCoss MJ. Assessing Protein Sequence Database Suitability Using De Novo Sequencing. Mol Cell Proteomics. 2020 Jan; 19 (1):198-208 Epub 2019 Nov 15
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43. Searle BC, Lawrence RT, MacCoss MJ, Villen J. Thesaurus: quantifying phosphopeptide positional isomers. Nat Methods. 2019 Aug; 16 (8):703-706 Epub 2019 July 29
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44. Pino LK, Searle BC, Yang HY. Team COUNCIL OF RICKS submission for EUPA YPIC 2017. EuPA Open Proteom. 2019 Mar; 22-23:22-24 Epub 2019 Oct 16
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45. Seitzer PM, Searle BC. Incorporating In-Source Fragment Information Improves Metabolite Identification Accuracy in Untargeted LC-MS Data Sets. J Proteome Res. 2019 Feb 1; 18 (2):791-796 Epub 2018 Oct 18
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46. Kim YJ, Sweet SMM, 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. J Proteome Res. 2019 Jan 4; 18 (1):426-435 Epub 2018 Dec 12
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47. Searle BC, Pino LK, Egertson JD, Ting YS, Lawrence RT, MacLean BX, Villen J, MacCoss MJ. Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry. Nat Commun. 2018 Dec 3; 9 (1):5128 Epub 2018 Dec 03
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48. Pino LK, Searle BC, Huang EL, Noble WS, Hoofnagle AN, MacCoss MJ. Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories. Anal Chem. 2018 Nov 6; 90 (21):13112-13117 Epub 2018 Oct 23
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49. 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. Nat Methods. 2017 Sep; 14 (9):903-908 Epub 2017 Aug 07
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50. Searle BC, Gittelman RM, Manor O, Akey JM. Detecting Sources of Transcriptional Heterogeneity in Large-Scale RNA-Seq Data Sets. Genetics. 2016 Dec; 204 (4):1391-1396 Epub 2016 Oct 11
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51. 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. 2016 Sep; 16 (18):2480-90
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52. Lawrence RT, Searle BC, Llovet A, Villen J. Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry. Nat Methods. 2016 May; 13 (5):431-4 Epub 2016 Mar 28
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53. 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. J Proteome Res. 2015 Oct 2; 14 (10):4169-78 Epub 2015 Sept 03
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54. 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 Sep; 14 (9):2331-40 Epub 2015 June 22
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55. Seymour SL, Farrah T, Binz PA, Chalkley RJ, Cottrell JS, Searle BC, Tabb DL, Vizcaino JA, Prieto G, Uszkoreit J, Eisenacher M, Martinez-Bartolome S, Ghali F, Jones AR. A standardized framing for reporting protein identifications in mzIdentML 1.2. Proteomics. 2014 Nov; 14 (21-22):2389-99 Epub 2014 Sept 23
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56. Ivanov AR, Colangelo CM, Dufresne CP, Friedman DB, Lilley KS, Mechtler K, Phinney BS, Rose KL, Rudnick PA, Searle BC, Shaffer SA, Weintraub ST. Interlaboratory studies and initiatives developing standards for proteomics. Proteomics. 2013 Mar; 13 (6):904-9 Epub 2013 Feb 19
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57. 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, Griss J, Vizcaino JA, Chambers M, Pizarro A, Creasy D. The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics. 2012 Jul; 11 (7):M111.014381 Epub 2012 Feb 27
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58. Eng JK, Searle BC, Clauser KR, Tabb DL. A face in the crowd: recognizing peptides through database search. Mol Cell Proteomics. 2011 Nov; 10 (11):R111.009522 Epub 2011 Aug 29
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59. Searle BC. Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies. Proteomics. 2010 Mar; 10 (6):1265-9
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60. Searle BC, Turner M, Nesvizhskii AI. Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies. J Proteome Res. 2008 Jan; 7 (1):245-53
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61. 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. J Proteome Res. 2005 Mar-Apr; 4 (2):546-54
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62. 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. Anal Chem. 2004 Apr 15; 76 (8):2220-30
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63. BuSha BF, Judd BG, Manning HL, Simon PM, Searle BC, Daubenspeck JA, Leiter JC. Identification of respiratory vagal feedback in awake normal subjects using pseudorandom unloading. J Appl Physiol (1985). 2001 Jun; 90 (6):2330-40
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