Michael J. MacCoss, Ph.D. - Publications

Affiliations: 
Genomic Sciences University of Washington, Seattle, Seattle, WA 

204 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
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  0.36
2019 Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, ... ... MacCoss MJ, et al. The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. Nucleic Acids Research. PMID 31686107 DOI: 10.1093/nar/gkz984  0.48
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  0.36
2019 Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews PC, Bernfur K, Borchers CH, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis TN, ... ... MacCoss MJ, et al. The First Community-Wide, Comparative Cross-linking Mass Spectrometry Study. Analytical Chemistry. PMID 31045356 DOI: 10.1021/acs.analchem.9b00658  0.84
2019 Amodei D, Egertson J, MacLean BX, Johnson R, Merrihew GE, Keller A, Marsh D, Vitek O, Mallick P, MacCoss MJ. Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows. Journal of the American Society For Mass Spectrometry. PMID 30671891 DOI: 10.1007/s13361-018-2122-8  0.44
2019 Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL. Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis. Molecular & Cellular Proteomics : McP. 18: 1-2. PMID 30602589 DOI: 10.1074/mcp.E118.001286  0.4
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  0.72
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  0.72
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  0.8
2018 Thomas RE, Vincow ES, Merrihew GE, MacCoss MJ, Davis MY, Pallanck LJ. Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles. Plos Genetics. 14: e1007694. PMID 30256786 DOI: 10.1371/journal.pgen.1007694  0.44
2018 Kruse A, Ramsey JS, Johnson R, Hall DG, MacCoss MJ, Heck M. 'Candidatus Liberibacter asiaticus' minimally alters expression of immunity and metabolism proteins in the hemolymph of Diaphorina citri, the insect vector of Huanglongbing. Journal of Proteome Research. PMID 30106293 DOI: 10.1021/acs.jproteome.8b00183  0.36
2018 MacLean BX, Pratt BS, Egertson JD, MacCoss MJ, Smith RD, Baker ES. Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions. Journal of the American Society For Mass Spectrometry. PMID 30047074 DOI: 10.1007/s13361-018-2028-5  0.72
2018 Claw KG, George RD, MacCoss MJ, Swanson WJ. Quantitative evolutionary proteomics of seminal fluid from primates with different mating systems. Bmc Genomics. 19: 488. PMID 29929489 DOI: 10.1186/s12864-018-4872-x  0.32
2018 Fong KK, Zelter A, Graczyk B, Hoyt JM, Riffle M, Johnson R, MacCoss MJ, Davis TN. Novel phosphorylation states of the yeast spindle pole body. Biology Open. PMID 29903865 DOI: 10.1242/bio.033647  0.36
2018 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, ... ... MacCoss MJ, et al. A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations. Cell Systems. PMID 29655704 DOI: 10.1016/j.cels.2018.03.012  0.72
2018 Tseng BS, Reichhardt C, Merrihew GE, Araujo-Hernandez SA, Harrison JJ, MacCoss MJ, Parsek MR. A Biofilm Matrix-Associated Protease Inhibitor Protects Pseudomonas aeruginosa from Proteolytic Attack. Mbio. 9. PMID 29636440 DOI: 10.1128/mBio.00543-18  0.44
2018 Peckner R, Myers SA, Jacome ASV, Egertson JD, Abelin JG, MacCoss MJ, Carr SA, Jaffe JD. Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics. Nature Methods. PMID 29608554 DOI: 10.1038/nmeth.4643  0.72
2018 Xu Y, Ju HJ, DeBlasio S, Carino EJ, Johnson R, MacCoss M, Heck MC, Miller WA, Gray SM. A stem-loop structure in potato leafroll virus ORF5 that is essential for readthrough translation of the coat protein ORF stop codon 700 bases upstream. Journal of Virology. PMID 29514911 DOI: 10.1128/JVI.01544-17  0.36
2018 Sharma V, Eckels J, Schilling B, Ludwig C, Jaffe JD, MacCoss MJ, MacLean B. Panorama Public: A public repository for quantitative data sets processed in Skyline. Molecular & Cellular Proteomics : McP. PMID 29487113 DOI: 10.1074/mcp.RA117.000543  0.48
2018 Galitzine C, Egertson J, Abbatiello SE, Henderson CM, Pino L, MacCoss MJ, Hoofnagle AN, Vitek O. Nonlinear regression improves accuracy of characterization of multiplexed mass spectrometric assays. Molecular & Cellular Proteomics : McP. PMID 29438992 DOI: 10.1074/mcp.RA117.000322  0.32
2017 Henderson CM, Shulman NJ, MacLean B, MacCoss MJ, Hoofnagle AN. Skyline Performs as Well as Vendor Software in the Quantitative Analysis of Serum 25-Hydroxy Vitamin D and Vitamin D Binding Globulin. Clinical Chemistry. PMID 29203474 DOI: 10.1373/clinchem.2017.282293  0.48
2017 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, et al. Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nature Methods. PMID 28825704 DOI: 10.1038/nmeth.4398  0.48
2017 DeBlasio SL, Bereman MS, Mahoney J, Thannhauser TW, Gray SM, MacCoss MJ, Cilia Heck M. Evaluation of a Bead-Free Coimmunoprecipitation Technique for Identification of Virus-Host Protein Interactions Using High-Resolution Mass Spectrometry. Journal of Biomolecular Techniques : Jbt. PMID 28785175 DOI: 10.7171/jbt.17-2803-002  0.44
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  0.8
2017 Goulding SP, Szumlinski KK, Contet C, MacCoss MJ, Wu CC. A mass spectrometry-based proteomic analysis of Homer2-interacting proteins in the mouse brain. Journal of Proteomics. PMID 28728878 DOI: 10.1016/j.jprot.2017.07.008  0.56
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  0.48
2017 Sakano H, Zorio DAR, Wang X, Ting YS, Noble WS, MacCoss MJ, Rubel EW, Wang Y. Proteomic analyses of nucleus laminaris identified candidate targets of the fragile X mental retardation protein. The Journal of Comparative Neurology. PMID 28685837 DOI: 10.1002/cne.24281  0.8
2017 Kruse A, Fattah-Hosseini S, Saha S, Johnson R, Warwick E, Sturgeon K, Mueller L, MacCoss MJ, Shatters RG, Cilia Heck M. Combining 'omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut. Plos One. 12: e0179531. PMID 28632769 DOI: 10.1371/journal.pone.0179531  0.36
2017 Zimmerman SG, Merrihew GE, MacCoss MJ, Berg CA. Proteomics Analysis Identifies Orthologs of Human Chitinase-Like Proteins as Inducers of Tube-Morphogenesis Defects in Drosophila. Genetics. PMID 28404605 DOI: 10.1534/genetics.116.199323  0.44
2017 Spencer SE, Corso TN, Bollinger JG, Henderson CM, Hoofnagle AN, MacCoss MJ. Automated Trapping Column Exchanger for High-Throughput Nanoflow Liquid Chromatography. Analytical Chemistry. PMID 28192907 DOI: 10.1021/acs.analchem.6b04227  0.36
2017 Kim JO, Zelter A, Umbreit NT, Bollozos A, Riffle M, Johnson R, MacCoss MJ, Asbury CL, Davis TN. The Ndc80 complex bridges two Dam1 complex rings. Elife. 6. PMID 28191870 DOI: 10.7554/eLife.21069  0.36
2017 Abbatiello SE, Ackermann BL, Borchers CH, Bradshaw RA, Carr SA, Chalkley RJ, Choi M, Deutsch EW, Domon B, Hoofnagle AN, Keshishian H, Kuhn E, Liebler DC, MacCoss MJ, MacLean B, et al. New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins. Molecular & Cellular Proteomics : McP. PMID 28183812 DOI: 10.1074/mcp.E117.067801  0.48
2017 Henderson CM, Bollinger JG, Becker JO, Wallace JM, Laha TJ, MacCoss MJ, Hoofnagle AN. Quantification by nano liquid chromatography-parallel reaction monitoring-mass spectrometry of human apolipoprotein A-I, apolipoprotein B, and hemoglobin A1c in dried blood spots. Proteomics. Clinical Applications. PMID 28112871 DOI: 10.1002/prca.201600103  0.36
2016 Berger S, Procko E, Margineantu D, Lee EF, Shen BW, Zelter A, Silva DA, Chawla K, Herold MJ, Garnier JM, Johnson R, MacCoss MJ, Lessene G, Davis TN, Stayton PS, et al. Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer. Elife. 5. PMID 27805565 DOI: 10.7554/eLife.20352  0.36
2016 Bereman MS, Beri J, Sharma V, Nathe C, Eckels J, MacLean B, MacCoss MJ. An Automated Pipeline to Monitor System Performance in Liquid Chromatography-Tandem Mass Spectrometry Proteomic Experiments. Journal of Proteome Research. PMID 27700092 DOI: 10.1021/acs.jproteome.6b00744  0.48
2016 The M, MacCoss MJ, Noble WS, Käll L. Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0. Journal of the American Society For Mass Spectrometry. PMID 27572102 DOI: 10.1007/s13361-016-1460-7  0.8
2016 Armbruster CR, Wolter DJ, Mishra M, Hayden HS, Radey MC, Merrihew G, MacCoss MJ, Burns J, Wozniak DJ, Parsek MR, Hoffman LR. Staphylococcus aureus Protein A Mediates Interspecies Interactions at the Cell Surface of Pseudomonas aeruginosa. Mbio. 7. PMID 27222468 DOI: 10.1128/mBio.00538-16  0.96
2016 Topalidou I, Cattin-Ortolá J, Pappas AL, Cooper K, Merrihew GE, MacCoss MJ, Ailion M. The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles. Plos Genetics. 12: e1006074. PMID 27191843 DOI: 10.1371/journal.pgen.1006074  0.96
2016 Basisty N, Dai DF, Gagnidze A, Gitari L, Fredrickson J, Maina Y, Beyer RP, Emond MJ, Hsieh EJ, MacCoss MJ, Martin GM, Rabinovitch PS. Mitochondrial-targeted catalase is good for the old mouse proteome, but not for the young: 'reverse' antagonistic pleiotropy? Aging Cell. PMID 27061426 DOI: 10.1111/acel.12472  0.96
2016 Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A. Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure. Journal of Structural Biology. PMID 26968363 DOI: 10.1016/j.jsb.2016.03.006  0.96
2016 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, ... ... MacCoss MJ, et al. Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays. Methods in Molecular Biology (Clifton, N.J.). 1410: 223-36. PMID 26867747 DOI: 10.1007/978-1-4939-3524-6_13  0.96
2016 Bollinger JG, Stergachis AB, Johnson RS, Egertson JD, MacCoss MJ. Selecting Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as Analytical Standards. Methods in Molecular Biology (Clifton, N.J.). 1410: 207-21. PMID 26867746 DOI: 10.1007/978-1-4939-3524-6_12  0.96
2015 Ramsey JS, Johnson RS, Hoki JS, Kruse A, Mahoney J, Hilf ME, Hunter WB, Hall DG, Schroeder FC, MacCoss MJ, Cilia M. Metabolic Interplay between the Asian Citrus Psyllid and Its Profftella Symbiont: An Achilles' Heel of the Citrus Greening Insect Vector. Plos One. 10: e0140826. PMID 26580079 DOI: 10.1371/journal.pone.0140826  0.96
2015 Zelter A, Bonomi M, Kim JO, Umbreit NT, Hoopmann MR, Johnson R, Riffle M, Jaschob D, MacCoss MJ, Moritz RL, Davis TN. The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling. Nature Communications. 6: 8673. PMID 26560693 DOI: 10.1038/ncomms9673  0.96
2015 Kawahara R, Bollinger JG, Rivera C, Ribeiro AC, Brandão TB, Leme AF, MacCoss MJ. A targeted proteomic strategy for the measurement of oral cancer candidate biomarkers in human saliva. Proteomics. PMID 26552850 DOI: 10.1002/pmic.201500224  0.36
2015 Kruse SE, Karunadharma PP, Basisty N, Johnson R, Beyer RP, MacCoss MJ, Rabinovitch PS, Marcinek DJ. Age modifies respiratory complex I and protein homeostasis in a muscle type-specific manner. Aging Cell. PMID 26498839 DOI: 10.1111/acel.12412  0.36
2015 Schilling B, MacLean B, Held JM, Sahu AK, Rardin MJ, Sorensen DJ, Peters T, Wolfe AJ, Hunter CL, MacCoss MJ, Gibson BW. Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows. Analytical Chemistry. PMID 26398777 DOI: 10.1021/acs.analchem.5b02983  0.96
2015 Ting YS, Egertson JD, Payne SH, Kim S, MacLean B, Käll L, Aebersold RH, Smith RD, Noble WS, MacCoss MJ. Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data. Molecular & Cellular Proteomics : McP. PMID 26217018 DOI: 10.1074/mcp.O114.047035  0.96
2015 Riffle M, Merrihew GE, Jaschob D, Sharma V, Davis TN, Noble WS, MacCoss MJ. Visualization and Dissemination of Multidimensional Proteomics Data Comparing Protein Abundance During Caenorhabditis elegans Development. Journal of the American Society For Mass Spectrometry. PMID 26133526 DOI: 10.1007/s13361-015-1193-z  0.96
2015 Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ. A Deeper Look into Comet-Implementation and Features. Journal of the American Society For Mass Spectrometry. PMID 26115965 DOI: 10.1007/s13361-015-1179-x  0.96
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  0.96
2015 Egertson JD, MacLean B, Johnson R, Xuan Y, MacCoss MJ. Multiplexed peptide analysis using data-independent acquisition and Skyline. Nature Protocols. 10: 887-903. PMID 25996789 DOI: 10.1038/nprot.2015.055  0.96
2015 Rardin MJ, Schilling B, Cheng LY, MacLean BX, Sorenson DJ, Sahu AK, MacCoss MJ, Vitek O, Gibson BW. MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments. Molecular & Cellular Proteomics : McP. PMID 25987414 DOI: 10.1074/mcp.O115.048181  0.96
2015 Karunadharma PP, Basisty N, Chiao YA, Dai DF, Drake R, Levy N, Koh WJ, Emond MJ, Kruse S, Marcinek D, Maccoss MJ, Rabinovitch PS. Respiratory chain protein turnover rates in mice are highly heterogeneous but strikingly conserved across tissues, ages, and treatments. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. PMID 25977255 DOI: 10.1096/fj.15-272666  0.96
2015 Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL. Kojak: efficient analysis of chemically cross-linked protein complexes. Journal of Proteome Research. 14: 2190-8. PMID 25812159 DOI: 10.1021/pr501321h  0.96
2015 Karunadharma PP, Basisty N, Dai DF, Chiao YA, Quarles EK, Hsieh EJ, Crispin D, Bielas JH, Ericson NG, Beyer RP, MacKay VL, MacCoss MJ, Rabinovitch PS. Subacute calorie restriction and rapamycin discordantly alter mouse liver proteome homeostasis and reverse aging effects. Aging Cell. 14: 547-57. PMID 25807975 DOI: 10.1111/acel.12317  0.44
2015 DeBlasio SL, Johnson R, Sweeney MM, Karasev A, Gray SM, MacCoss MJ, Cilia M. Potato leafroll virus structural proteins manipulate overlapping, yet distinct protein interaction networks during infection. Proteomics. 15: 2098-112. PMID 25787689 DOI: 10.1002/pmic.201400594  0.96
2015 Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Ghosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, ... ... MacCoss MJ, et al. Large-scale inter-laboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma. Molecular & Cellular Proteomics : McP. PMID 25693799 DOI: 10.1074/mcp.M114.047050  0.96
2015 DeBlasio SL, Johnson R, Mahoney J, Karasev A, Gray SM, MacCoss MJ, Cilia M. Insights into the polerovirus-plant interactome revealed by coimmunoprecipitation and mass spectrometry. Molecular Plant-Microbe Interactions : Mpmi. 28: 467-81. PMID 25496593 DOI: 10.1094/MPMI-11-14-0363-R  0.96
2015 Kim TY, Siesser PF, Rossman KL, Goldfarb D, Mackinnon K, Yan F, Yi X, MacCoss MJ, Moon RT, Der CJ, Major MB. Substrate trapping proteomics reveals targets of the βTrCP2/FBXW11 ubiquitin ligase. Molecular and Cellular Biology. 35: 167-81. PMID 25332235 DOI: 10.1128/MCB.00857-14  0.96
2014 Song YH, Estrada DA, Johnson RS, Kim SK, Lee SY, MacCoss MJ, Imaizumi T. Distinct roles of FKF1, Gigantea, and Zeitlupe proteins in the regulation of Constans stability in Arabidopsis photoperiodic flowering. Proceedings of the National Academy of Sciences of the United States of America. 111: 17672-7. PMID 25422419 DOI: 10.1073/pnas.1415375111  0.96
2014 Marsillach J, Suzuki SM, Richter RJ, McDonald MG, Rademacher PM, MacCoss MJ, Hsieh EJ, Rettie AE, Furlong CE. Human valacyclovir hydrolase/biphenyl hydrolase-like protein is a highly efficient homocysteine thiolactonase. Plos One. 9: e110054. PMID 25333274 DOI: 10.1371/journal.pone.0110054  0.96
2014 Canterbury JD, Merrihew GE, MacCoss MJ, Goodlett DR, Shaffer SA. Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics. Journal of the American Society For Mass Spectrometry. 25: 2048-59. PMID 25261218 DOI: 10.1007/s13361-014-0981-1  0.52
2014 Tien JF, Umbreit NT, Zelter A, Riffle M, Hoopmann MR, Johnson RS, Fonslow BR, Yates JR, MacCoss MJ, Moritz RL, Asbury CL, Davis TN. Kinetochore biorientation in Saccharomyces cerevisiae requires a tightly folded conformation of the Ndc80 complex. Genetics. 198: 1483-93. PMID 25230952 DOI: 10.1534/genetics.114.167775  0.84
2014 McIlwain S, Tamura K, Kertesz-Farkas A, Grant CE, Diament B, Frewen B, Howbert JJ, Hoopmann MR, Käll L, Eng JK, MacCoss MJ, Noble WS. Crux: rapid open source protein tandem mass spectrometry analysis. Journal of Proteome Research. 13: 4488-91. PMID 25182276 DOI: 10.1021/pr500741y  0.96
2014 Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, ... ... MacCoss M, et al. Comparative analysis of the transcriptome across distant species. Nature. 512: 445-8. PMID 25164755 DOI: 10.1038/nature13424  0.96
2014 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, et al. Panorama: a targeted proteomics knowledge base. Journal of Proteome Research. 13: 4205-10. PMID 25102069 DOI: 10.1021/pr5006636  0.96
2014 Damodarasamy M, Johnson RS, Bentov I, MacCoss MJ, Vernon RB, Reed MJ. Hyaluronan enhances wound repair and increases collagen III in aged dermal wounds. Wound Repair and Regeneration : Official Publication of the Wound Healing Society [and] the European Tissue Repair Society. 22: 521-6. PMID 25041621 DOI: 10.1111/wrr.12192  0.96
2014 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, Paulovich AG. CPTAC Assay Portal: a repository of targeted proteomic assays. Nature Methods. 11: 703-4. PMID 24972168 DOI: 10.1038/nmeth.3002  0.96
2014 Cilia M, Johnson R, Sweeney M, DeBlasio SL, Bruce JE, MacCoss MJ, Gray SM. Evidence for lysine acetylation in the coat protein of a polerovirus Journal of General Virology. 95: 2321-2329. PMID 24939649 DOI: 10.1099/vir.0.066514-0  0.96
2014 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, ... ... MacCoss MJ, et al. A framework for installable external tools in Skyline. Bioinformatics (Oxford, England). 30: 2521-3. PMID 24813211 DOI: 10.1093/bioinformatics/btu148  0.96
2014 Dai DF, Karunadharma PP, Chiao YA, Basisty N, Crispin D, Hsieh EJ, Chen T, Gu H, Djukovic D, Raftery D, Beyer RP, MacCoss MJ, Rabinovitch PS. Altered proteome turnover and remodeling by short-term caloric restriction or rapamycin rejuvenate the aging heart. Aging Cell. 13: 529-39. PMID 24612461 DOI: 10.1111/acel.12203  0.96
2014 Pinheiro P, Bereman MS, Burd J, Pals M, Armstrong S, Howe KJ, Thannhauser TW, MacCoss MJ, Gray SM, Cilia M. Evidence of the biochemical basis of host virulence in the greenbug aphid, Schizaphis graminum (Homoptera: Aphididae). Journal of Proteome Research. 13: 2094-108. PMID 24588548 DOI: 10.1021/pr4012415  0.96
2014 Bereman MS, Johnson R, Bollinger J, Boss Y, Shulman N, MacLean B, Hoofnagle AN, MacCoss MJ. Implementation of statistical process control for proteomic experiments via LC MS/MS. Journal of the American Society For Mass Spectrometry. 25: 581-7. PMID 24496601 DOI: 10.1007/s13361-013-0824-5  0.96
2014 Fujimoto GM, Monroe ME, Rodriguez L, Wu C, MacLean B, Smith RD, MacCoss MJ, Payne SH. Accounting for population variation in targeted proteomics. Journal of Proteome Research. 13: 321-3. PMID 24320210 DOI: 10.1021/pr4011052  0.96
2014 Bateman NW, Goulding SP, Shulman NJ, Gadok AK, Szumlinski KK, MacCoss MJ, Wu CC. Maximizing peptide identification events in proteomic workflows using data-dependent acquisition (DDA) Molecular and Cellular Proteomics. 13: 329-338. PMID 23820513 DOI: 10.1074/mcp.M112.026500  0.96
2014 Woo S, Cha SW, Merrihew G, He Y, Castellana N, Guest C, MacCoss M, Bafna V. Proteogenomic database construction driven from large scale RNA-seq data. Journal of Proteome Research. 13: 21-8. PMID 23802565 DOI: 10.1021/pr400294c  0.96
2014 Canterbury JD, Merrihew GE, MacCoss MJ, Goodlett DR, Shaffer SA. Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics Journal of the American Society For Mass Spectrometry. 25: 2048-2059. DOI: 10.1007/s13361-014-0981-1  0.96
2013 Aagaard JE, George RD, Fishman L, Maccoss MJ, Swanson WJ. Selection on plant male function genes identifies candidates for reproductive isolation of yellow monkeyflowers. Plos Genetics. 9: e1003965. PMID 24339787 DOI: 10.1371/journal.pgen.1003965  0.96
2013 Tamborindeguy C, Bereman MS, DeBlasio S, Igwe D, Smith DM, White F, MacCoss MJ, Gray SM, Cilia M. Genomic and proteomic analysis of Schizaphis graminum reveals cyclophilin proteins are involved in the transmission of cereal yellow dwarf virus. Plos One. 8: e71620. PMID 23951206 DOI: 10.1371/journal.pone.0071620  0.96
2013 Dai DF, Hsieh EJ, Chen T, Menendez LG, Basisty NB, Tsai L, Beyer RP, Crispin DA, Shulman NJ, Szeto HH, Tian R, MacCoss MJ, Rabinovitch PS. Global proteomics and pathway analysis of pressure-overload-induced heart failure and its attenuation by mitochondrial-targeted peptides. Circulation. Heart Failure. 6: 1067-76. PMID 23935006 DOI: 10.1161/CIRCHEARTFAILURE.113.000406  0.96
2013 Schleit J, Johnson SC, Bennett CF, Simko M, Trongtham N, Castanza A, Hsieh EJ, Moller RM, Wasko BM, Delaney JR, Sutphin GL, Carr D, Murakami CJ, Tocchi A, Xian B, ... ... MacCoss MJ, et al. Molecular mechanisms underlying genotype-dependent responses to dietary restriction. Aging Cell. 12: 1050-61. PMID 23837470 DOI: 10.1111/acel.12130  0.96
2013 Conlon KP, Basrur V, Rolland D, Wolfe T, Nesvizhskii AI, MacCoss MJ, Lim MS, Elenitoba-Johnson KSJ. Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer Molecular and Cellular Proteomics. 12: 2714-2723. PMID 23836920 DOI: 10.1074/mcp.M113.029926  0.96
2013 Egertson JD, Kuehn A, Merrihew GE, Bateman NW, MacLean BX, Ting YS, Canterbury JD, Marsh DM, Kellmann M, Zabrouskov V, Wu CC, MacCoss MJ. Multiplexed MS/MS for improved data-independent acquisition Nature Methods. 10: 744-746. PMID 23793237 DOI: 10.1038/nmeth.2528  0.96
2013 Skelly DA, Merrihew GE, Riffle M, Connelly CF, Kerr EO, Johansson M, Jaschob D, Graczyk B, Shulman NJ, Wakefield J, Cooper SJ, Fields S, Noble WS, Muller EG, Davis TN, ... ... Maccoss MJ, et al. Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. Genome Research. 23: 1496-504. PMID 23720455 DOI: 10.1101/gr.155762.113  0.96
2013 Glukhova VA, Tomazela DM, Findlay GD, Monnat RJ, MacCoss MJ. Rapid assessment of RNAi-mediated protein depletion by selected reaction monitoring mass spectrometry. Journal of Proteome Research. 12: 3246-54. PMID 23713831 DOI: 10.1021/pr400067k  0.96
2013 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, ... ... Maccoss M, et al. 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). Molecular & Cellular Proteomics : McP. 12: 2623-39. PMID 23689285 DOI: 10.1074/mcp.M112.027078  0.96
2013 Goulding SP, MacCoss MJ, Wu CC. Label-free differential analysis of murine postsynaptic densities Methods in Molecular Biology. 1002: 295-309. PMID 23625411 DOI: 10.1007/978-1-62703-360-2_22  0.96
2013 Palmer MR, McDowall MH, Stewart L, Ouaddi A, MacCoss MJ, Swanson WJ. Mass spectrometry and next-generation sequencing reveal an abundant and rapidly evolving abalone sperm protein. Molecular Reproduction and Development. 80: 460-5. PMID 23585193 DOI: 10.1002/mrd.22182  0.96
2013 Vincow ES, Merrihew G, Thomas RE, Shulman NJ, Beyer RP, MacCoss MJ, Pallanck LJ. The PINK1-Parkin pathway promotes both mitophagy and selective respiratory chain turnover in vivo. Proceedings of the National Academy of Sciences of the United States of America. 110: 6400-5. PMID 23509287 DOI: 10.1073/pnas.1221132110  0.96
2013 Chan MM, Wooden JM, Tsang M, Gilligan DM, Hirenallur-S DK, Finney GL, Rynes E, Maccoss M, Ramirez JA, Park H, Iritani BM. Hematopoietic protein-1 regulates the actin membrane skeleton and membrane stability in murine erythrocytes. Plos One. 8: e54902. PMID 23424621 DOI: 10.1371/journal.pone.0054902  0.96
2013 Bereman MS, Hsieh EJ, Corso TN, Van Pelt CK, MacCoss MJ. Development and characterization of a novel plug and play liquid chromatography-mass spectrometry (LC-MS) source that automates connections between the capillary trap, column, and emitter Molecular and Cellular Proteomics. 12: 1701-1708. PMID 23422586 DOI: 10.1074/mcp.O112.024893  0.96
2013 Hsieh EJ, Bereman MS, Durand S, Valaskovic GA, MacCoss MJ. Effects of column and gradient lengths on peak capacity and peptide identification in nanoflow LC-MS/MS of complex proteomic samples. Journal of the American Society For Mass Spectrometry. 24: 148-53. PMID 23197307 DOI: 10.1007/s13361-012-0508-6  0.96
2013 Marsillach J, Hsieh EJ, Richter RJ, MacCoss MJ, Furlong CE. Proteomic analysis of adducted butyrylcholinesterase for biomonitoring organophosphorus exposures. Chemico-Biological Interactions. 203: 85-90. PMID 23123252 DOI: 10.1016/j.cbi.2012.10.019  0.96
2012 McIlwain S, Mathews M, Bereman MS, Rubel EW, MacCoss MJ, Noble WS. Estimating relative abundances of proteins from shotgun proteomics data. Bmc Bioinformatics. 13: 308. PMID 23164367 DOI: 10.1186/1471-2105-13-308  0.96
2012 Cilia M, Peter KA, Bereman MS, Howe K, Fish T, Smith D, Gildow F, MacCoss MJ, Thannhauser TW, Gray SM. Discovery and Targeted LC-MS/MS of Purified Polerovirus Reveals Differences in the Virus-Host Interactome Associated with Altered Aphid Transmission Plos One. 7. PMID 23118947 DOI: 10.1371/journal.pone.0048177  0.96
2012 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, ... ... MacCoss M, et al. A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology. 30: 918-20. PMID 23051804 DOI: 10.1038/nbt.2377  0.96
2012 Egertson JD, Eng JK, Bereman MS, Hsieh EJ, Merrihew GE, MacCoss MJ. De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics Journal of the American Society For Mass Spectrometry. 23: 2075-2082. PMID 23007965 DOI: 10.1007/s13361-012-0482-z  0.96
2012 Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, ... ... MacCoss MJ, et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature. 489: 83-90. PMID 22955618 DOI: 10.1038/nature11212  0.96
2012 Spivak M, Bereman MS, Maccoss MJ, Noble WS. Learning score function parameters for improved spectrum identification in tandem mass spectrometry experiments. Journal of Proteome Research. 11: 4499-508. PMID 22866926 DOI: 10.1021/pr300234m  0.96
2012 Hsieh EJ, Shulman NJ, Dai DF, Vincow ES, Karunadharma PP, Pallanck L, Rabinovitch PS, MacCoss MJ. Topograph, a software platform for precursor enrichment corrected global protein turnover measurements. Molecular & Cellular Proteomics : McP. 11: 1468-74. PMID 22865922 DOI: 10.1074/mcp.O112.017699  0.96
2012 Sharma V, Eng JK, MacCoss MJ, Riffle M. A mass spectrometry proteomics data management platform Molecular and Cellular Proteomics. 11: 824-831. PMID 22611296 DOI: 10.1074/mcp.O111.015149  0.96
2012 Bereman MS, Maclean B, Tomazela DM, Liebler DC, Maccoss MJ. The development of selected reaction monitoring methods for targeted proteomics via empirical refinement Proteomics. 12: 1134-1141. PMID 22577014 DOI: 10.1002/pmic.201200042  0.96
2012 Escher C, Reiter L, Maclean B, Ossola R, Herzog F, Chilton J, Maccoss MJ, Rinner O. Using iRT, a normalized retention time for more targeted measurement of peptides Proteomics. 12: 1111-1121. PMID 22577012 DOI: 10.1002/pmic.201100463  0.96
2012 Sherrod SD, Myers MV, Li M, Myers JS, Carpenter KL, Maclean B, Maccoss MJ, Liebler DC, Ham AJ. Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptides. Journal of Proteome Research. 11: 3467-79. PMID 22559222 DOI: 10.1021/pr201240a  0.96
2012 Bereman MS, Tomazela DM, Heins HS, Simonato M, Cogo PE, Hamvas A, Patterson BW, Cole FS, MacCoss MJ. A method to determine the kinetics of multiple proteins in human infants with respiratory distress syndrome Analytical and Bioanalytical Chemistry. 403: 2397-2402. PMID 22526637 DOI: 10.1007/s00216-012-5953-3  0.96
2012 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. Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation. Molecular & Cellular Proteomics : McP. 11: 202-14. PMID 22454539 DOI: 10.1074/mcp.M112.017707  0.96
2012 Gilligan DM, Finney GL, Rynes E, MacCoss MJ, Lambert AJ, Peters LL, Robledo RF, Wooden JM. Retraction notice to "Comparative proteomics reveals deficiency of NHE-1 (Slc9a1) in RBCs from the beta-adducin knockout mouse model of hemolytic anemia" [Blood Cells Mol. Dis. 47 (2011) 85-94] Blood Cells, Molecules, and Diseases. 48: 145. PMID 22393569 DOI: 10.1016/j.bcmd.2011.12.007  0.96
2012 Hoopmann MR, MacCoss MJ, Moritz RL. Identification of peptide features in precursor spectra using hardklör and krönik Current Protocols in Bioinformatics. PMID 22389013 DOI: 10.1002/0471250953.bi1318s37  0.96
2012 Noble WS, MacCoss MJ. Computational and statistical analysis of protein mass spectrometry data. Plos Computational Biology. 8: e1002296. PMID 22291580 DOI: 10.1371/journal.pcbi.1002296  0.96
2012 Wojcik R, Li Y, Maccoss MJ, Dovichi NJ. Capillary electrophoresis with Orbitrap-Velos mass spectrometry detection. Talanta. 88: 324-9. PMID 22265506 DOI: 10.1016/j.talanta.2011.10.048  0.96
2012 Bereman MS, Canterbury JD, Egertson JD, Horner J, Remes PM, Schwartz J, Zabrouskov V, MacCoss MJ. Evaluation of front-end higher energy collision-induced dissociation on a benchtop dual-pressure linear ion trap mass spectrometer for shotgun proteomics Analytical Chemistry. 84: 1533-1539. PMID 22192247 DOI: 10.1021/ac203210a  0.96
2012 Spivak M, Weston J, Tomazela D, MacCoss MJ, Noble WS. Direct maximization of protein identifications from tandem mass spectra. Molecular & Cellular Proteomics : McP. 11: M111.012161. PMID 22052992 DOI: 10.1074/mcp.M111.012161  0.96
2012 Dai DF, Hsieh EJ, Liu Y, Chen T, Beyer RP, Chin MT, MacCoss MJ, Rabinovitch PS. Mitochondrial proteome remodelling in pressure overload-induced heart failure: The role of mitochondrial oxidative stress Cardiovascular Research. 93: 79-88. PMID 22012956 DOI: 10.1093/cvr/cvr274  0.96
2012 Cilia M, Bereman M, Fish T, MacCoss MJ, Gray S. Homopteran Vector Biomarkers for Efficient Circulative Plant Virus Transmission are Conserved in Multiple Aphid Species and the Whitefly Bemisia tabaci Journal of Integrative Agriculture. 11: 249-262. DOI: 10.1016/S2095-3119(12)60009-4  0.96
2011 Stergachis AB, MacLean B, Lee K, Stamatoyannopoulos JA, MacCoss MJ. Rapid empirical discovery of optimal peptides for targeted proteomics Nature Methods. 8: 1041-1046. PMID 22056677 DOI: 10.1038/nmeth.1770  0.96
2011 Pierce SB, Spurrell CH, Mandell JB, Lee MK, Zeligson S, Bereman MS, Stray SM, Fokstuen S, MacCoss MJ, Levy-Lahad E, King MC, Motulsky AG. Garrod's fourth inborn error of metabolism solved by the identification of mutations causing pentosuria. Proceedings of the National Academy of Sciences of the United States of America. 108: 18313-7. PMID 22042873 DOI: 10.1073/pnas.1115888108  0.96
2011 Marsillach J, Richter RJ, Kim JH, Stevens RC, MacCoss MJ, Tomazela D, Suzuki SM, Schopfer LM, Lockridge O, Furlong CE. Biomarkers of organophosphorus (OP) exposures in humans. Neurotoxicology. 32: 656-60. PMID 21767566 DOI: 10.1016/j.neuro.2011.06.005  0.96
2011 Wooden JM, Finney GL, Rynes E, Maccoss MJ, Lambert AJ, Robledo RF, Peters LL, Gilligan DM. Comparative proteomics reveals deficiency of SLC9A1 (sodium/hydrogen exchanger NHE1) in β-adducin null red cells. British Journal of Haematology. 154: 492-501. PMID 21689084 DOI: 10.1111/j.1365-2141.2011.08612.x  0.96
2011 Dean MD, Findlay GD, Hoopmann MR, Wu CC, MacCoss MJ, Swanson WJ, Nachman MW. Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling. Bmc Genomics. 12: 306. PMID 21663664 DOI: 10.1186/1471-2164-12-306  0.96
2011 Bereman MS, Egertson JD, Maccoss MJ. Comparison between procedures using SDS for shotgun proteomic analyses of complex samples Proteomics. 11: 2931-2935. PMID 21656683 DOI: 10.1002/pmic.201100045  0.96
2011 Gilligan DM, Finney GL, Rynes E, Maccoss MJ, Lambert AJ, Peters LL, Robledo RF, Wooden JM. Comparative proteomics reveals deficiency of NHE-1 (Slc9a1) in RBCs from the beta-adducin knockout mouse model of hemolytic anemia. Blood Cells, Molecules & Diseases. 47: 85-94. PMID 21592827 DOI: 10.1016/j.bcmd.2011.03.008  0.96
2011 Falick AM, Lane WS, Lilley KS, MacCoss MJ, Phinney BS, Sherman NE, Weintraub ST, Witkowska HE, Yates NA. ABRF-PRG07: advanced quantitative proteomics study. Journal of Biomolecular Techniques : Jbt. 22: 21-6. PMID 21455478  0.96
2011 Friedman DB, Andacht TM, Bunger MK, Chien AS, Hawke DH, Krijgsveld J, Lane WS, Lilley KS, MacCoss MJ, Moritz RL, Settlage RE, Sherman NE, Weintraub ST, Witkowska HE, Yates NA, et al. The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses. Proteomics. 11: 1371-81. PMID 21394914 DOI: 10.1002/pmic.201000736  0.96
2010 Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, ... ... MacCoss M, et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (New York, N.Y.). 330: 1775-87. PMID 21177976 DOI: 10.1126/science.1196914  0.96
2010 MacLean B, Tomazela DM, Abbatiello SE, Zhang S, Whiteaker JR, Paulovich AG, Carr SA, MacCoss MJ. Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry Analytical Chemistry. 82: 10116-10124. PMID 21090646 DOI: 10.1021/ac102179j  0.96
2010 Ranjitkar P, Press MO, Yi X, Baker R, MacCoss MJ, Biggins S. An E3 Ubiquitin Ligase Prevents Ectopic Localization of the Centromeric Histone H3 Variant via the Centromere Targeting Domain Molecular Cell. 40: 455-464. PMID 21070971 DOI: 10.1016/j.molcel.2010.09.025  0.96
2010 Sharma V, Eng JK, Feldman S, von Haller PD, MacCoss MJ, Noble WS. Precursor charge state prediction for electron transfer dissociation tandem mass spectra. Journal of Proteome Research. 9: 5438-44. PMID 20731383 DOI: 10.1021/pr1006685  0.96
2010 Serang O, MacCoss MJ, Noble WS. Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data. Journal of Proteome Research. 9: 5346-57. PMID 20712337 DOI: 10.1021/pr100594k  0.96
2010 Kelley JL, Aagaard JE, MacCoss MJ, Swanson WJ. Functional diversification and evolution of antifreeze proteins in the antarctic fish Lycodichthys dearborni. Journal of Molecular Evolution. 71: 111-8. PMID 20686757 DOI: 10.1007/s00239-010-9367-6  0.96
2010 Rosenfeld RJ, Bonaventura J, Szymczyna BR, MacCoss MJ, Arvai AS, Yates JR, Tainer JA, Getzoff ED. Nitric-oxide synthase forms N-NO-pterin and S-NO-cys: implications for activity, allostery, and regulation. The Journal of Biological Chemistry. 285: 31581-9. PMID 20659888 DOI: 10.1074/jbc.M109.072496  0.36
2010 Chakrabarti L, Zahra R, Jackson SM, Kazemi-Esfarjani P, Sopher BL, Mason AG, Toneff T, Ryu S, Shaffer S, Kansy JW, Eng J, Merrihew G, MacCoss MJ, Murphy A, Goodlett DR, et al. Mitochondrial dysfunction in NnaD mutant flies and Purkinje cell degeneration mice reveals a role for Nna proteins in neuronal bioenergetics. Neuron. 66: 835-47. PMID 20620870 DOI: 10.1016/j.neuron.2010.05.024  0.96
2010 Cooper SJ, Finney GL, Brown SL, Nelson SK, Hesselberth J, MacCoss MJ, Fields S. High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection. Genome Research. 20: 1288-96. PMID 20610602 DOI: 10.1101/gr.105825.110  0.96
2010 Zelter A, Hoopmann MR, Vernon R, Baker D, MacCoss MJ, Davis TN. Isotope signatures allow identification of chemically cross-linked peptides by mass spectrometry: A novel method to determine interresidue distances in protein structures through cross-linking Journal of Proteome Research. 9: 3583-3589. PMID 20476776 DOI: 10.1021/pr1001115  0.96
2010 Canterbury JD, Gladden J, Buck L, Olund R, MacCoss MJ. A high voltage asymmetric waveform generator for FAIMS. Journal of the American Society For Mass Spectrometry. 21: 1118-21. PMID 20332067 DOI: 10.1016/j.jasms.2010.02.019  0.96
2010 Kim JH, Stevens RC, MacCoss MJ, Goodlett DR, Scherl A, Richter RJ, Suzuki SM, Furlong CE. Identification and characterization of biomarkers of organophosphorus exposures in humans. Advances in Experimental Medicine and Biology. 660: 61-71. PMID 20221871 DOI: 10.1007/978-1-60761-350-3_7  0.96
2010 Tomazela DM, Patterson BW, Hanson E, Sponce KL, Kanion TB, Salinger DH, Vicini P, Barret H, Heins HB, Sessions Cole F, Hamvas A, MacCoss MJ. Measurement of human surfactant protein-B turnover in vivo from tracheal aspirates using targeted proteomics Analytical Chemistry. 82: 2561-2567. PMID 20178338 DOI: 10.1021/ac1001433  0.96
2010 MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics (Oxford, England). 26: 966-8. PMID 20147306 DOI: 10.1093/bioinformatics/btq054  0.96
2010 Bern M, Finney G, Hoopmann MR, Merrihew G, Toth MJ, MacCoss MJ. Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry. Analytical Chemistry. 82: 833-41. PMID 20039681 DOI: 10.1021/ac901801b  0.96
2010 Hsieh EJ, Hoopmann MR, MacLean B, MacCoss MJ. Comparison of database search strategies for high precursor mass accuracy MS/MS data Journal of Proteome Research. 9: 1138-1143. PMID 19938873 DOI: 10.1021/pr900816a  0.96
2010 Aagaard JE, Vacquier VD, MacCoss MJ, Swanson WJ. ZP domain proteins in the abalone egg coat include a paralog of VERL under positive selection that binds lysin and 18-kDa sperm proteins. Molecular Biology and Evolution. 27: 193-203. PMID 19767347 DOI: 10.1093/molbev/msp221  0.96
2010 Li Q, MacCoss MJ, Stephens M. A nested mixture model for protein identification using mass spectrometry Annals of Applied Statistics. 4: 962-987. DOI: 10.1214/09-AOAS316  0.96
2009 Second TP, Blethrow JD, Schwartz JC, Merrihew GE, MacCoss MJ, Swaney DL, Russell JD, Coon JJ, Zabrouskov V. Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Analytical Chemistry. 81: 7757-65. PMID 19689114 DOI: 10.1021/ac901278y  0.96
2009 Patiño S, Aagaard JE, MacCoss MJ, Swanson WJ, Hart MW. Bindin from a sea star. Evolution & Development. 11: 376-81. PMID 19601971 DOI: 10.1111/j.1525-142X.2009.00344.x  0.96
2009 Dai DF, Santana LF, Vermulst M, Tomazela DM, Emond MJ, MacCoss MJ, Gollahon K, Martin GM, Loeb LA, Ladiges WC, Rabinovitch PS. Overexpression of catalase targeted to mitochondria attenuates murine cardiac aging. Circulation. 119: 2789-97. PMID 19451351 DOI: 10.1161/CIRCULATIONAHA.108.822403  0.96
2009 Dean MD, Clark NL, Findlay GD, Karn RC, Yi X, Swanson WJ, MacCoss MJ, Nachman MW. Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus). Molecular Biology and Evolution. 26: 1733-43. PMID 19420050 DOI: 10.1093/molbev/msp094  0.96
2009 Findlay GD, MacCoss MJ, Swanson WJ. Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila. Genome Research. 19: 886-96. PMID 19411605 DOI: 10.1101/gr.089391.108  0.96
2009 Prakash A, Tomazela DM, Frewen B, MacLean B, Merrihew G, Peterman S, MacCoss MJ. Expediting the development of targeted SRM assays: Using data from shotgun proteomics to automate method development Journal of Proteome Research. 8: 2733-2739. PMID 19326923 DOI: 10.1021/pr801028b  0.96
2009 Hoopmann MR, Merrihew GE, Von Haller PD, MacCoss MJ. Post analysis data acquisition for the Iterative MS/MS sampling of proteomics mixtures Journal of Proteome Research. 8: 1870-1875. PMID 19256536 DOI: 10.1021/pr800828p  0.96
2008 MacCoss MJ, Wu CC. Proteomic solutions for analytical challenges associated with alcohol research Alcohol Research and Health. 31: 251-255. PMID 23584870  0.96
2008 Kline KG, Frewen B, Bristow MR, Maccoss MJ, Wu CC. High quality catalog of proteotypic peptides from human heart. Journal of Proteome Research. 7: 5055-61. PMID 18803417 DOI: 10.1021/pr800239e  0.96
2008 Eng JK, Fischer B, Grossmann J, MacCoss MJ. A fast SEQUEST cross correlation algorithm Journal of Proteome Research. 7: 4598-4602. PMID 18774840 DOI: 10.1021/pr800420s  0.96
2008 Canterbury JD, Yi X, Hoopmann MR, MacCoss MJ. Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics Analytical Chemistry. 80: 6888-6897. PMID 18693747 DOI: 10.1021/ac8004988  0.96
2008 Findlay GD, Yi X, Maccoss MJ, Swanson WJ. Proteomics reveals novel Drosophila seminal fluid proteins transferred at mating. Plos Biology. 6: e178. PMID 18666829 DOI: 10.1371/journal.pbio.0060178  0.96
2008 Merrihew GE, Davis C, Ewing B, Williams G, Käll L, Frewen BE, Noble WS, Green P, Thomas JH, MacCoss MJ. Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Research. 18: 1660-9. PMID 18653799 DOI: 10.1101/gr.077644.108  0.96
2008 Klammer AA, Reynolds SM, Bilmes JA, MacCoss MJ, Noble WS. Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. Bioinformatics (Oxford, England). 24: i348-56. PMID 18586734 DOI: 10.1093/bioinformatics/btn189  0.96
2008 Park CY, Klammer AA, Käll L, MacCoss MJ, Noble WS. Rapid and accurate peptide identification from tandem mass spectra. Journal of Proteome Research. 7: 3022-7. PMID 18505281 DOI: 10.1021/pr800127y  0.96
2008 Finney GL, Blackler AR, Hoopmann MR, Canterbury JD, Wu CC, MacCoss MJ. Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution μLC-MS data Analytical Chemistry. 80: 961-971. PMID 18189369 DOI: 10.1021/ac701649e  0.96
2008 Käll L, Storey JD, MacCoss MJ, Noble WS. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. Journal of Proteome Research. 7: 29-34. PMID 18067246 DOI: 10.1021/pr700600n  0.96
2008 Käll L, Storey JD, MacCoss MJ, Noble WS. Posterior error probabilities and false discovery rates: two sides of the same coin. Journal of Proteome Research. 7: 40-4. PMID 18052118 DOI: 10.1021/pr700739d  0.96
2007 Frewen B, MacCoss MJ. Using BiblioSpec for creating and searching tandem MS peptide libraries. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 13.7. PMID 18428681 DOI: 10.1002/0471250953.bi1307s20  0.96
2007 Käll L, Canterbury JD, Weston J, Noble WS, MacCoss MJ. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nature Methods. 4: 923-5. PMID 17952086 DOI: 10.1038/nmeth1113  0.96
2007 Mayor T, Graumann J, Bryan J, MacCoss MJ, Deshaies RJ. Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway. Molecular & Cellular Proteomics : McP. 6: 1885-95. PMID 17644757 DOI: 10.1074/mcp.M700264-MCP200  0.96
2007 Clark NL, Findlay GD, Yi X, MacCoss MJ, Swanson WJ. Duplication and selection on abalone sperm lysin in an allopatric population. Molecular Biology and Evolution. 24: 2081-90. PMID 17630281 DOI: 10.1093/molbev/msm137  0.96
2007 Klammer AA, Yi X, MacCoss MJ, Noble WS. Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions. Analytical Chemistry. 79: 6111-8. PMID 17622186 DOI: 10.1021/ac070262k  0.96
2007 Hoopmann MR, Finney GL, MacCoss MJ. High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry. Analytical Chemistry. 79: 5620-32. PMID 17580982 DOI: 10.1021/ac0700833  0.96
2007 Major MB, Camp ND, Berndt JD, Yi X, Goldenberg SJ, Hubbert C, Biechele TL, Gingras AC, Zheng N, Maccoss MJ, Angers S, Moon RT. Wilms tumor suppressor WTX negatively regulates WNT/beta-catenin signaling. Science (New York, N.Y.). 316: 1043-6. PMID 17510365 DOI: 10.1126/science/1141515  0.96
2007 Wu CC, MacCoss MJ. Quantitative proteomic analysis of mammalian organisms using metabolically labeled tissues. Methods in Molecular Biology (Clifton, N.J.). 359: 191-201. PMID 17484119 DOI: 10.1007/978-1-59745-255-7_13  0.96
2007 MacCoss MJ, Wu CC. Computational analysis of quantitative proteomics data using stable isotope labeling. Methods in Molecular Biology (Clifton, N.J.). 359: 177-89. PMID 17484118 DOI: 10.1007/978-1-59745-255-7_12  0.96
2007 Eakin CM, Maccoss MJ, Finney GL, Klevit RE. Estrogen receptor alpha is a putative substrate for the BRCA1 ubiquitin ligase. Proceedings of the National Academy of Sciences of the United States of America. 104: 5794-9. PMID 17392432 DOI: 10.1073/pnas.0610887104  0.96
2007 Wegner DJ, Hertzberg T, Heins HB, Elmberger G, MacCoss MJ, Carlson CS, Nogee LM, Cole FS, Hamvas A. A major deletion in the surfactant protein-B gene causing lethal respiratory distress. Acta Paediatrica (Oslo, Norway : 1992). 96: 516-20. PMID 17391469 DOI: 10.1111/j.1651-2227.2006.00188.x  0.96
2007 Klammer AA, Yi X, MacCoss MJ, Noble WS. Peptide retention time prediction yields improved tandem mass spectrum identification for diverse chromatography conditions Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4453: 459-472.  0.96
2006 Aagaard JE, Yi X, MacCoss MJ, Swanson WJ. Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs. Proceedings of the National Academy of Sciences of the United States of America. 103: 17302-7. PMID 17085584 DOI: 10.1073/pnas.0603125103  0.96
2006 Angers S, Li T, Yi X, MacCoss MJ, Moon RT, Zheng N. Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery. Nature. 443: 590-3. PMID 16964240 DOI: 10.1038/nature05175  0.96
2006 Frewen BE, Merrihew GE, Wu CC, Noble WS, MacCoss MJ. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Analytical Chemistry. 78: 5678-84. PMID 16906711 DOI: 10.1021/ac060279n  0.96
2006 Angers S, Thorpe CJ, Biechele TL, Goldenberg SJ, Zheng N, MacCoss MJ, Moon RT. The KLHL12-Cullin-3 ubiquitin ligase negatively regulates the Wnt-beta-catenin pathway by targeting Dishevelled for degradation. Nature Cell Biology. 8: 348-57. PMID 16547521 DOI: 10.1038/ncb1381  0.96
2006 Klammer AA, MacCoss MJ. Effects of modified digestion schemes on the identification of proteins from complex mixtures. Journal of Proteome Research. 5: 695-700. PMID 16512685 DOI: 10.1021/pr050315j  0.96
2006 Blackler AR, Klammer AA, MacCoss MJ, Wu CC. Quantitative comparison of proteomic data quality between a 2D and 3D quadrupole ion trap. Analytical Chemistry. 78: 1337-44. PMID 16478131 DOI: 10.1021/ac051486a  0.96
2005 Klammer AA, Wu CC, MacCoss MJ, Noble WS. Peptide charge state determination for low-resolution tandem mass spectra. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 175-85. PMID 16447975 DOI: 10.1109/CSB.2005.44  0.96
2005 MacCoss MJ, Wu CC, Matthews DE, Yates JR. Measurement of the isotope enrichment of stable isotope-labeled proteins using high-resolution mass spectra of peptides Analytical Chemistry. 77: 7646-7653. PMID 16316172 DOI: 10.1021/ac0508393  0.96
2005 MacCoss MJ, Matthews DE. Qantitative MS for proteomics: Teaching a new dog old tricks Analytical Chemistry. 77: 294 A-302 A. PMID 16134292  0.96
2005 Hoffman LR, D'Argenio DA, MacCoss MJ, Zhang Z, Jones RA, Miller SI. Aminoglycoside antibiotics induce bacterial biofilm formation. Nature. 436: 1171-5. PMID 16121184 DOI: 10.1038/nature03912  0.96
2005 MacCoss MJ. Computational analysis of shotgun proteomics data Current Opinion in Chemical Biology. 9: 88-94. PMID 15701459 DOI: 10.1016/j.cbpa.2004.12.010  0.96
2004 Wu CC, MacCoss MJ, Howell KE, Matthews DE, Yates JR. Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis Analytical Chemistry. 76: 4951-4959. PMID 15373428 DOI: 10.1021/ac049208j  0.96
2004 McDonald WH, Tabb DL, Sadygov RG, MacCoss MJ, Venable J, Graumann J, Johnson JR, Cociorva D, Yates JR. MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Communications in Mass Spectrometry : Rcm. 18: 2162-8. PMID 15317041 DOI: 10.1002/rcm.1603  0.96
2004 Anderson LB, Ouellette AJ, Eaton-Rye J, Maderia M, MacCoss MJ, Yates JR, Barry BA. Evidence for a post-translational modification, aspartyl aldehyde, in a photosynthetic membrane protein. Journal of the American Chemical Society. 126: 8399-405. PMID 15237995 DOI: 10.1021/ja0478781  0.96
2004 Wu CC, MacCoss MJ, Mardones G, Finnigan C, Mogelsvang S, Yates JR, Howell KE. Organellar proteomics reveals Golgi arginine dimethylation Molecular Biology of the Cell. 15: 2907-2919. PMID 15047867 DOI: 10.1091/mbc.E04-02-0101  0.96
2003 MacCoss MJ, Wu CC, Liu H, Sadygov R, Yates JR. A Correlation Algorithm for the Automated Quantitative Analysis of Shotgun Proteomics Data Analytical Chemistry. 75: 6912-6921. PMID 14670053 DOI: 10.1021/ac034790h  0.96
2003 Tabb DL, MacCoss MJ, Wu CC, Anderson SD, Yates JR. Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Analytical Chemistry. 75: 2470-7. PMID 12918992 DOI: 10.1021/ac026424o  0.96
2003 Wu CC, MacCoss MJ, Howell KE, Yates JR. A method for the comprehensive proteomic analysis of membrane proteins Nature Biotechnology. 21: 532-538. PMID 12692561 DOI: 10.1038/nbt819  0.96
2002 Sadygov RG, Eng J, Durr E, Saraf A, McDonald H, MacCoss MJ, Yates JR. Code developments to improve the efficiency of automated MS/MS spectra interpretation. Journal of Proteome Research. 1: 211-5. PMID 12645897 DOI: 10.1021/pr015514r  0.96
2002 Anderson LB, Maderia M, Ouellette AJ, Putnam-Evans C, Higgins L, Krick T, MacCoss MJ, Lim H, Yates JR, Barry BA. Posttranslational modifications in the CP43 subunit of photosystem II. Proceedings of the National Academy of Sciences of the United States of America. 99: 14676-81. PMID 12417747 DOI: 10.1073/pnas.232591599  0.96
2002 Wu CC, MacCoss MJ. Shotgun proteomics: Tools for the analysis of complex biological systems Current Opinion in Molecular Therapeutics. 4: 242-250. PMID 12139310  0.96
2002 MacCoss MJ, McDonald WH, Saraf A, Sadygov R, Clark JM, Tasto JJ, Gould KL, Wolters D, Washburn M, Weiss A, Clark JI, Yates JR. Shotgun identification of protein modifications from protein complexes and lens tissue. Proceedings of the National Academy of Sciences of the United States of America. 99: 7900-5. PMID 12060738 DOI: 10.1073/pnas.122231399  0.96
2002 MacCoss MJ, Wu CC, Yates JR. Probability based validation of protein identifications using a modified SEQUEST algorithm Analytical Chemistry. 74: 5593-5599. DOI: 10.1021/ac025826t  0.96
2002 Wu CC, MacCoss MJ, Howell KE, Yates JR. Proteomic analysis of Golgi membrane proteins: Identification, topology, and covalent modifications Proceedings 50th Asms Conference On Mass Spectrometry and Allied Topics. 99-100.  0.96
2002 MacCoss MJ, Wu CC, Yates JR. Measurement of proteome-wide protein kinetics Proceedings 50th Asms Conference On Mass Spectrometry and Allied Topics. 57-58.  0.96
2001 MacCoss MJ, Yates JR. Proteomics: Analytical tools and techniques Current Opinion in Clinical Nutrition and Metabolic Care. 4: 369-375. PMID 11568497 DOI: 10.1097/00075197-200109000-00006  0.96
2001 Maccoss MJ, Toth MJ, Matthews DE. Evaluation and optimization of ion-current ratio measurements by selected-ion-monitoring mass spectrometry Analytical Chemistry. 73: 2976-2984. PMID 11467543 DOI: 10.1021/ac010041t  0.96
2001 Toth MJ, MacCoss MJ, Poehlman ET, Matthews DE. Recovery of 13CO2 from infused [1-13C]leucine and [1,2-13C2]leucine in healthy humans American Journal of Physiology - Endocrinology and Metabolism. 281: E233-E241. PMID 11440898  0.96
2001 MacCoss MJ, Fukagawa NK, Matthews DE. Measurement of intracellular sulfur amino acid metabolism in humans American Journal of Physiology - Endocrinology and Metabolism. 280: E947-E955. PMID 11350776  0.96
2001 Toth MJ, Poehlman ET, Matthews DE, Tchernof A, MacCoss MJ. Effects of estradiol and progesterone on body composition, protein synthesis, and lipoprotein lipase in rats American Journal of Physiology - Endocrinology and Metabolism. 280: E496-E501. PMID 11171605  0.96
1999 MacCoss MJ, Fukagawa NK, Matthews DE. Measurement of homocysteine concentrations and stable isotope tracer enrichments in human plasma Analytical Chemistry. 71: 4527-4533. PMID 10546531 DOI: 10.1021/ac990541a  0.96
1995 Griffin PR, MacCoss MJ, Eng JK, Blevins RA, Aaronson JS, Yates JR. Direct database searching with MALDI-PSD spectra of peptides Rapid Communications in Mass Spectrometry. 9: 1546-1551. PMID 8652878  0.96
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