For those interested in numbers, see Brian’s Google Scholar citations profile.

If you cannot access one of our papers, let us know and we’ll try to help.


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. doi: 10.1021/acs.jproteome.0c00964. Epub 2021 Mar 17. PMID: 33729787.


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. doi: 10.1021/acs.jproteome.0c00685. Epub 2020 Sep 23. PMID: 32966080.

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. doi: 10.1074/mcp.P119.001913. Epub 2020 Apr 20. PMID: 32312845; PMCID: PMC7338082.

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. doi: 10.7171/jbt.20-3101-003. PMID: 31969795; PMCID: PMC6959150.

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. Nat Commun. 2020 Mar 25;11(1):1548. doi: 10.1038/s41467-020-15346-1. PMID: 32214105; PMCID: PMC7096433.

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. doi: 10.1016/j.celrep.2020.01.096. PMID: 32101728.

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. doi: 10.1021/acs.jproteome.9b00666. Epub 2020 Feb 24. PMID: 32037841; PMCID: PMC7175947.

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. doi: 10.1074/mcp.TIR119.001752. Epub 2019 Nov 15. PMID: 31732549; PMCID: PMC6944239.


Searle BC, Lawrence RT, MacCoss MJ, Villén J. Thesaurus: quantifying phosphopeptide positional isomers. Nat Methods. 2019 Aug;16(8):703-706. doi: 10.1038/s41592-019-0498-4. Epub 2019 Jul 29. PMID: 31363206; PMCID: PMC7012383.

Searle BC, Yergey AL. An efficient solution for resolving iTRAQ and TMT channel cross-talk. J Mass Spectrom. 2020 Aug;55(8):e4354. doi: 10.1002/jms.4354. Epub 2019 Apr 29. PMID: 30882954.

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. doi: 10.1021/acs.jproteome.8b00699. Epub 2018 Dec 12. PMID: 30481034; PMCID: PMC6465117.


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. Nat Commun. 2018 Dec 3;9(1):5128. doi: 10.1038/s41467-018-07454-w. PMID: 30510204; PMCID: PMC6277451.

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. doi: 10.1021/acs.analchem.8b04581. Epub 2018 Oct 23. PMID: 30350613; PMCID: PMC6854904.

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. doi: 10.1021/acs.jproteome.8b00601. Epub 2018 Oct

  1. PMID: 30295490.


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. doi: 10.1038/nmeth.4390. Epub 2017 Aug 7. PMID: 28783153; PMCID: PMC5578911.

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. doi: 10.1002/mas.21540. Epub 2017 Jul 9. PMID: 28691345; PMCID: PMC5799042.


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. doi: 10.1534/genetics.116.193714. Epub 2016 Oct 11. PMID: 27729424; PMCID: PMC5161273.

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. doi: 10.1002/pmic.201600137. PMID: 27546229; PMCID: PMC5176252.

Lawrence RT, Searle BC, Llovet A, Villén J. Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry. Nat Methods. 2016 May;13(5):431-4. doi: 10.1038/nmeth.3811. Epub 2016 Mar 28. PMID: 27018578; PMCID: PMC5915315.


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. doi: 10.1021/acs.jproteome.5b00254. Epub 2015 Sep 3. PMID: 26288259; PMCID: PMC5571863.

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. doi: 10.1074/mcp.M115.051300. Epub 2015 Jun 22. PMID: 26100116; PMCID: PMC4563719.


Seymour SL, Farrah T, Binz PA, Chalkley RJ, Cottrell JS, Searle BC, Tabb DL, Vizcaíno JA, Prieto G, Uszkoreit J, Eisenacher M, Martínez-Bartolomé S, Ghali F, Jones AR. A standardized framing for reporting protein identifications in mzIdentML 1.2. Proteomics. 2014 Nov;14(21-22):2389-99. doi: 10.1002/pmic.201400080. Epub 2014 Sep 23. PMID: 25092112; PMCID: PMC4384534.


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. doi: 10.1002/pmic.201200532. Epub 2013 Feb 19. PMID: 23319436; PMCID: PMC3863631.


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, Vizcaíno 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. doi: 10.1074/mcp.M111.014381. Epub 2012 Feb 27. PMID: 22375074; PMCID: PMC3394945.


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. doi: 10.1074/mcp.R111.009522. Epub 2011 Aug 29. PMID: 21876205; PMCID: PMC3226415.

2010 and earlier

Searle BC. Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies. Proteomics. 2010 Mar;10(6):1265-9. doi: 10.1002/pmic.200900437. PMID: 20077414.

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. doi: 10.1021/pr070540w. PMID: 18173222.

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. doi: 10.1021/pr049781j. PMID: 15822933.

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. doi: 10.1021/ac035258x. PMID: 15080731.