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Items: 1 to 50 of 93

1.

Standardization of PGC-LC-MS-based glycomics for sample specific glycotyping.

Ashwood C, Pratt B, MacLean BX, Gundry RL, Packer NH.

Analyst. 2019 Jun 7;144(11):3601-3612. doi: 10.1039/c9an00486f. Epub 2019 May 8.

PMID:
31065629
2.

Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows.

Amodei D, Egertson J, MacLean BX, Johnson R, Merrihew GE, Keller A, Marsh D, Vitek O, Mallick P, MacCoss MJ.

J Am Soc Mass Spectrom. 2019 Apr;30(4):669-684. doi: 10.1007/s13361-018-2122-8. Epub 2019 Jan 22.

3.

Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry.

Searle BC, Pino LK, Egertson JD, Ting YS, Lawrence RT, MacLean BX, Villén J, MacCoss MJ.

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

4.

Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions.

MacLean BX, Pratt BS, Egertson JD, MacCoss MJ, Smith RD, Baker ES.

J Am Soc Mass Spectrom. 2018 Nov;29(11):2182-2188. doi: 10.1007/s13361-018-2028-5. Epub 2018 Jul 25.

PMID:
30047074
5.

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations.

Litichevskiy L, Peckner R, Abelin JG, Asiedu JK, Creech AL, Davis JF, Davison D, Dunning CM, Egertson JD, Egri S, Gould J, Ko T, Johnson SA, Lahr DL, Lam D, Liu Z, Lyons NJ, Lu X, MacLean BX, Mungenast AE, Officer A, Natoli TE, Papanastasiou M, Patel J, Sharma V, Toder C, Tubelli AA, Young JZ, Carr SA, Golub TR, Subramanian A, MacCoss MJ, Tsai LH, Jaffe JD.

Cell Syst. 2018 Apr 25;6(4):424-443.e7. doi: 10.1016/j.cels.2018.03.012. Epub 2018 Apr 11.

6.

Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline.

Sharma V, Eckels J, Schilling B, Ludwig C, Jaffe JD, MacCoss MJ, MacLean B.

Mol Cell Proteomics. 2018 Jun;17(6):1239-1244. doi: 10.1074/mcp.RA117.000543. Epub 2018 Feb 27.

7.

Spatial trends in a biomagnifying contaminant: Application of amino acid compound-specific stable nitrogen isotope analysis to the interpretation of bird mercury levels.

Dolgova S, Popp BN, Courtoreille K, Espie RHM, Maclean B, McMaster M, Straka JR, Tetreault GR, Wilkie S, Hebert CE.

Environ Toxicol Chem. 2018 May;37(5):1466-1475. doi: 10.1002/etc.4113. Epub 2018 Apr 14.

PMID:
29446488
8.

Skyline Performs as Well as Vendor Software in the Quantitative Analysis of Serum 25-Hydroxy Vitamin D and Vitamin D Binding Globulin.

Henderson CM, Shulman NJ, MacLean B, MacCoss MJ, Hoofnagle AN.

Clin Chem. 2018 Feb;64(2):408-410. doi: 10.1373/clinchem.2017.282293. Epub 2017 Dec 4. No abstract available.

9.

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses.

Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, Aebersold R.

Nat Methods. 2017 Sep;14(9):921-927. doi: 10.1038/nmeth.4398. Epub 2017 Aug 21.

10.

The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics.

Pino LK, Searle BC, Bollinger JG, Nunn B, MacLean B, MacCoss MJ.

Mass Spectrom Rev. 2017 Jul 9. doi: 10.1002/mas.21540. [Epub ahead of print] Review.

11.

MSstatsQC: Longitudinal System Suitability Monitoring and Quality Control for Targeted Proteomic Experiments.

Dogu E, Mohammad-Taheri S, Abbatiello SE, Bereman MS, MacLean B, Schilling B, Vitek O.

Mol Cell Proteomics. 2017 Jul;16(7):1335-1347. doi: 10.1074/mcp.M116.064774. Epub 2017 May 8.

12.

New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins.

Abbatiello S, Ackermann BL, Borchers C, Bradshaw RA, Carr SA, Chalkley R, Choi M, Deutsch E, Domon B, Hoofnagle AN, Keshishian H, Kuhn E, Liebler DC, MacCoss M, MacLean B, Mani DR, Neubert H, Smith D, Vitek O, Zimmerman L.

Mol Cell Proteomics. 2017 Mar;16(3):327-328. doi: 10.1074/mcp.E117.067801. Epub 2017 Feb 9. No abstract available.

13.

ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments.

Choi M, Eren-Dogu ZF, Colangelo C, Cottrell J, Hoopmann MR, Kapp EA, Kim S, Lam H, Neubert TA, Palmblad M, Phinney BS, Weintraub ST, MacLean B, Vitek O.

J Proteome Res. 2017 Feb 3;16(2):945-957. doi: 10.1021/acs.jproteome.6b00881. Epub 2017 Jan 3.

PMID:
27990823
14.

A multicenter study benchmarks software tools for label-free proteome quantification.

Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S.

Nat Biotechnol. 2016 Nov;34(11):1130-1136. doi: 10.1038/nbt.3685. Epub 2016 Oct 3.

15.

An Automated Pipeline to Monitor System Performance in Liquid Chromatography-Tandem Mass Spectrometry Proteomic Experiments.

Bereman MS, Beri J, Sharma V, Nathe C, Eckels J, MacLean B, MacCoss MJ.

J Proteome Res. 2016 Dec 2;15(12):4763-4769. Epub 2016 Oct 4.

16.

Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays.

Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Boja E, Carr SA, Chan DW, Chen X, Chen J, Davies SR, Ellis MJ, Fenyö D, Hiltke T, Ketchum KA, Kinsinger C, Kuhn E, Liebler DC, Liu T, Loss M, MacCoss MJ, Qian WJ, Rivers R, Rodland KD, Ruggles KV, Scott MG, Smith RD, Thomas S, Townsend RR, Whiteley G, Wu C, Zhang H, Zhang Z, Rodriguez H, Paulovich AG.

Methods Mol Biol. 2016;1410:223-36. doi: 10.1007/978-1-4939-3524-6_13.

17.

Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows.

Schilling B, MacLean B, Held JM, Sahu AK, Rardin MJ, Sorensen DJ, Peters T, Wolfe AJ, Hunter CL, MacCoss MJ, Gibson BW.

Anal Chem. 2015 Oct 20;87(20):10222-9. doi: 10.1021/acs.analchem.5b02983. Epub 2015 Sep 30.

18.

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data.

Ting YS, Egertson JD, Payne SH, Kim S, MacLean B, Käll L, Aebersold R, Smith RD, Noble WS, MacCoss MJ.

Mol Cell Proteomics. 2015 Sep;14(9):2301-7. doi: 10.1074/mcp.O114.047035. Epub 2015 Jul 27.

19.

Public health response to a large-scale endoscopy infection control lapse in a nonhospital clinic.

Willmore J, Ellis E, Etches V, Labrecque L, Osiowy C, Andonov A, McDermaid C, Majury A, Achonu C, Maher M, MacLean B, Levy I.

Can J Infect Dis Med Microbiol. 2015 Mar-Apr;26(2):77-84.

20.

Multiplexed peptide analysis using data-independent acquisition and Skyline.

Egertson JD, MacLean B, Johnson R, Xuan Y, MacCoss MJ.

Nat Protoc. 2015 Jun;10(6):887-903. doi: 10.1038/nprot.2015.055. Epub 2015 May 21.

21.

MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments.

Rardin MJ, Schilling B, Cheng LY, MacLean BX, Sorensen DJ, Sahu AK, MacCoss MJ, Vitek O, Gibson BW.

Mol Cell Proteomics. 2015 Sep;14(9):2405-19. doi: 10.1074/mcp.O115.048181. Epub 2015 May 17.

22.

Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma.

Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA.

Mol Cell Proteomics. 2015 Sep;14(9):2357-74. doi: 10.1074/mcp.M114.047050. Epub 2015 Feb 18.

23.

Building high-quality assay libraries for targeted analysis of SWATH MS data.

Schubert OT, Gillet LC, Collins BC, Navarro P, Rosenberger G, Wolski WE, Lam H, Amodei D, Mallick P, MacLean B, Aebersold R.

Nat Protoc. 2015 Mar;10(3):426-41. doi: 10.1038/nprot.2015.015. Epub 2015 Feb 12.

PMID:
25675208
24.

Panorama: a targeted proteomics knowledge base.

Sharma V, Eckels J, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Yan P, Whiteaker JR, Halusa GN, Schilling B, Gibson BW, Colangelo CM, Paulovich AG, Carr SA, Jaffe JD, MacCoss MJ, MacLean B.

J Proteome Res. 2014 Sep 5;13(9):4205-10. doi: 10.1021/pr5006636. Epub 2014 Aug 18.

25.

CPTAC Assay Portal: a repository of targeted proteomic assays.

Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Rodriguez H; Clinical Proteomic Tumor Analysis Consortium (CPTAC), Paulovich AG.

Nat Methods. 2014 Jul;11(7):703-4. doi: 10.1038/nmeth.3002. No abstract available.

26.

A framework for installable external tools in Skyline.

Broudy D, Killeen T, Choi M, Shulman N, Mani DR, Abbatiello SE, Mani D, Ahmad R, Sahu AK, Schilling B, Tamura K, Boss Y, Sharma V, Gibson BW, Carr SA, Vitek O, MacCoss MJ, MacLean B.

Bioinformatics. 2014 Sep 1;30(17):2521-3. doi: 10.1093/bioinformatics/btu148. Epub 2014 May 9.

27.

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments.

Choi M, Chang CY, Clough T, Broudy D, Killeen T, MacLean B, Vitek O.

Bioinformatics. 2014 Sep 1;30(17):2524-6. doi: 10.1093/bioinformatics/btu305. Epub 2014 May 2.

PMID:
24794931
28.

Implementation of statistical process control for proteomic experiments via LC MS/MS.

Bereman MS, Johnson R, Bollinger J, Boss Y, Shulman N, MacLean B, Hoofnagle AN, MacCoss MJ.

J Am Soc Mass Spectrom. 2014 Apr;25(4):581-7. doi: 10.1007/s13361-013-0824-5. Epub 2014 Feb 5.

29.

Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.

Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S.

Mol Cell Proteomics. 2014 Mar;13(3):907-17. doi: 10.1074/mcp.M113.036095. Epub 2014 Jan 17.

30.

Accounting for population variation in targeted proteomics.

Fujimoto GM, Monroe ME, Rodriguez L, Wu C, MacLean B, Smith RD, MacCoss MJ, Payne SH.

J Proteome Res. 2014 Jan 3;13(1):321-3. doi: 10.1021/pr4011052. Epub 2013 Dec 16.

31.

Multiplexed MS/MS for improved data-independent acquisition.

Egertson JD, Kuehn A, Merrihew GE, Bateman NW, MacLean BX, Ting YS, Canterbury JD, Marsh DM, Kellmann M, Zabrouskov V, Wu CC, MacCoss MJ.

Nat Methods. 2013 Aug;10(8):744-6. doi: 10.1038/nmeth.2528. Epub 2013 Jun 23.

32.

Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS).

Abbatiello SE, Mani DR, Schilling B, Maclean B, Zimmerman LJ, Feng X, Cusack MP, Sedransk N, Hall SC, Addona T, Allen S, Dodder NG, Ghosh M, Held JM, Hedrick V, Inerowicz HD, Jackson A, Keshishian H, Kim JW, Lyssand JS, Riley CP, Rudnick P, Sadowski P, Shaddox K, Smith D, Tomazela D, Wahlander A, Waldemarson S, Whitwell CA, You J, Zhang S, Kinsinger CR, Mesri M, Rodriguez H, Borchers CH, Buck C, Fisher SJ, Gibson BW, Liebler D, Maccoss M, Neubert TA, Paulovich A, Regnier F, Skates SJ, Tempst P, Wang M, Carr SA.

Mol Cell Proteomics. 2013 Sep;12(9):2623-39. doi: 10.1074/mcp.M112.027078. Epub 2013 May 20.

33.

A cross-platform toolkit for mass spectrometry and proteomics.

Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, Baker TA, Brusniak MY, Paulse C, Creasy D, Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, Lefebvre B, Kuhlmann F, Roark J, Rainer P, Detlev S, Hemenway T, Huhmer A, Langridge J, Connolly B, Chadick T, Holly K, Eckels J, Deutsch EW, Moritz RL, Katz JE, Agus DB, MacCoss M, Tabb DL, Mallick P.

Nat Biotechnol. 2012 Oct;30(10):918-20. doi: 10.1038/nbt.2377. No abstract available.

34.

The role of bridging ligand in hydrogen generation by photocatalytic Ru/Pd assemblies.

Bindra GS, Schulz M, Paul A, Groarke R, Soman S, Inglis JL, Browne WR, Pfeffer MG, Rau S, MacLean BJ, Pryce MT, Vos JG.

Dalton Trans. 2012 Nov 14;41(42):13050-9. doi: 10.1039/c2dt30948c.

PMID:
23014910
35.

The development of selected reaction monitoring methods for targeted proteomics via empirical refinement.

Bereman MS, MacLean B, Tomazela DM, Liebler DC, MacCoss MJ.

Proteomics. 2012 Apr;12(8):1134-41. doi: 10.1002/pmic.201200042. Review.

36.

Using iRT, a normalized retention time for more targeted measurement of peptides.

Escher C, Reiter L, MacLean B, Ossola R, Herzog F, Chilton J, MacCoss MJ, Rinner O.

Proteomics. 2012 Apr;12(8):1111-21. doi: 10.1002/pmic.201100463.

37.

Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptides.

Sherrod SD, Myers MV, Li M, Myers JS, Carpenter KL, Maclean B, Maccoss MJ, Liebler DC, Ham AJ.

J Proteome Res. 2012 Jun 1;11(6):3467-79. doi: 10.1021/pr201240a. Epub 2012 May 17.

38.

Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation.

Schilling B, Rardin MJ, MacLean BX, Zawadzka AM, Frewen BE, Cusack MP, Sorensen DJ, Bereman MS, Jing E, Wu CC, Verdin E, Kahn CR, Maccoss MJ, Gibson BW.

Mol Cell Proteomics. 2012 May;11(5):202-14. doi: 10.1074/mcp.M112.017707. Epub 2012 Mar 26.

39.

Seroprevalence of hepatitis B surface antigen among pregnant women attending the Hospital for Women & Children in Koutiala, Mali.

MacLean B, Hess RF, Bonvillain E, Kamate J, Dao D, Cosimano A, Hoy S.

S Afr Med J. 2011 Dec 14;102(1):47-9.

PMID:
22273139
40.

Rapid empirical discovery of optimal peptides for targeted proteomics.

Stergachis AB, MacLean B, Lee K, Stamatoyannopoulos JA, MacCoss MJ.

Nat Methods. 2011 Nov 6;8(12):1041-3. doi: 10.1038/nmeth.1770.

41.

Guest editorial: equine-assisted therapy.

MacLean B.

J Rehabil Res Dev. 2011;48(7):ix-xii. No abstract available.

42.

The effect of peripheral bipyridine ligands on the photocatalytic hydrogen production activity of Ru/Pd catalysts.

Singh Bindra G, Schulz M, Paul A, Soman S, Groarke R, Inglis J, Pryce MT, Browne WR, Rau S, Maclean BJ, Vos JG.

Dalton Trans. 2011 Nov 7;40(41):10812-4. doi: 10.1039/c1dt11241d. Epub 2011 Sep 9.

PMID:
21904769
43.

Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry.

Maclean B, Tomazela DM, Abbatiello SE, Zhang S, Whiteaker JR, Paulovich AG, Carr SA, Maccoss MJ.

Anal Chem. 2010 Dec 15;82(24):10116-24. doi: 10.1021/ac102179j. Epub 2010 Nov 19.

44.

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.

MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ.

Bioinformatics. 2010 Apr 1;26(7):966-8. doi: 10.1093/bioinformatics/btq054. Epub 2010 Feb 9.

45.

Anisocoria and topical carbamate exposure: illustrative case report.

Upshaw J, MacLean B, Losek JD.

Clin Pediatr (Phila). 2010 May;49(5):502-5. doi: 10.1177/0009922809338512. Epub 2010 Jan 28. No abstract available.

PMID:
20118074
46.

Comparison of database search strategies for high precursor mass accuracy MS/MS data.

Hsieh EJ, Hoopmann MR, MacLean B, MacCoss MJ.

J Proteome Res. 2010 Feb 5;9(2):1138-43. doi: 10.1021/pr900816a.

47.

Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development.

Prakash A, Tomazela DM, Frewen B, Maclean B, Merrihew G, Peterman S, Maccoss MJ.

J Proteome Res. 2009 Jun;8(6):2733-9. doi: 10.1021/pr801028b.

48.

Precursor-ion mass re-estimation improves peptide identification on hybrid instruments.

Luethy R, Kessner DE, Katz JE, Maclean B, Grothe R, Kani K, Faça V, Pitteri S, Hanash S, Agus DB, Mallick P.

J Proteome Res. 2008 Sep;7(9):4031-9. doi: 10.1021/pr800307m. Epub 2008 Aug 16.

49.

General framework for developing and evaluating database scoring algorithms using the TANDEM search engine.

MacLean B, Eng JK, Beavis RC, McIntosh M.

Bioinformatics. 2006 Nov 15;22(22):2830-2. Epub 2006 Jul 28.

PMID:
16877754
50.

Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments.

Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, Maclean B, Lin CW, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whiteaker J, States D, Hanash S, Paulovich A, McIntosh MW.

J Proteome Res. 2006 Jan;5(1):112-21. Erratum in: J Proteome Res. 2006 Apr;5(4):1024. Whitaker, Jeffrey [corrected to Whiteaker, Jeffrey].

PMID:
16396501

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