Publications

2024

Hybrid Quadrupole Mass Filter-Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics Remes PM, Jacob CC, Heil LR, Shulman N, MacLean BX, MacCoss MJ Journal of proteome research 2024 Dec;23(12):5476-5486 PubMed | DOI

Detection and Quantification of Drug-Protein Adducts in Human Liver Zelter A, Riffle M, Shteynberg DD, Zhong G, Riddle EB, Hoopmann MR, Jaschob D, Moritz RL, Davis TN, MacCoss MJ, Isoherranen N Journal of proteome research 2024 Nov;23(11):5143-5152 PubMed | DOI

Data-independent acquisition proteomic analysis of the brain microvasculature in Alzheimer’s disease identifies major pathways of dysfunction and upregulation of cytoprotective responses Erickson MA, Johnson RS, Damodarasamy M, MacCoss MJ, Keene CD, Banks WA, Reed MJ Fluids and barriers of the CNS 2024 Oct;21(1):84 PubMed | DOI

Tissue-specific metabolomic signatures for a doublesex model of reduced sexual dimorphism Coig R, Harrison BR, Johnson RS, MacCoss MJ, Promislow DEL bioRxiv : the preprint server for biology 2024 Sep PubMed | DOI

A Framework for Quality Control in Quantitative Proteomics Tsantilas KA, Merrihew GE, Robbins JE, Johnson RS, Park J, Plubell DL, Canterbury JD, Huang E, Riffle M, Sharma V, MacLean BX, Eckels J, Wu CC, Bereman MS, Spencer SE, Hoofnagle AN, MacCoss MJ Journal of proteome research 2024 Oct;23(10):4392-4408 PubMed | DOI

NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data Thangudu RR, Holck M, Singhal D, Pilozzi A, Edwards N, Rudnick PA, Domagalski MJ, Chilappagari P, Ma L, Xin Y, Le T, Nyce K, Chaudhary R, Ketchum KA, Maurais A, Connolly B, Riffle M, Chambers MC, MacLean B, MacCoss MJ, McGarvey PB, Basu A, Otridge J, Casas-Silva E, Venkatachari S, Rodriguez H, Zhang X Cancer research communications 2024 Sep;4(9):2480-2488 PubMed | DOI

Mouse sarcopenia model reveals sex- and age-specific differences in phenotypic and molecular characteristics Kerr HL, Krumm K, Anderson B, Christiani A, Strait L, Li T, Irwin B, Jiang S, Rybachok A, Chen A, Dacek E, Caeiro L, Merrihew GE, MacDonald JW, Bammler TK, MacCoss MJ, Garcia JM The Journal of clinical investigation 2024 Jun;134(16) PubMed | DOI

A second X chromosome improves cognition in aging male and female mice Marino F, Wang D, Merrihew GE, MacCoss MJ, Dubal DB bioRxiv : the preprint server for biology 2024 Jul PubMed | DOI

Development of highly multiplex targeted proteomics assays in biofluids using the Stellar mass spectrometer Plubell DL, Remes PM, Wu CC, Jacob CC, Merrihew GE, Hsu C, Shulman N, MacLean BX, Heil L, Poston K, Montine T, MacCoss MJ bioRxiv : the preprint server for biology 2024 Jun PubMed | DOI

Hybrid Quadrupole Mass Filter - Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics Remes PM, Jacob CC, Heil LR, Shulman N, MacLean BX, MacCoss MJ bioRxiv : the preprint server for biology 2024 Jun PubMed | DOI

Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer Plubell DL, Huang E, Spencer SE, Poston K, Montine TJ, MacCoss MJ bioRxiv : the preprint server for biology 2024 May PubMed | DOI

A framework for quality control in quantitative proteomics Tsantilas KA, Merrihew GE, Robbins JE, Johnson RS, Park J, Plubell DL, Canterbury JD, Huang E, Riffle M, Sharma V, MacLean BX, Eckels J, Wu CC, Bereman MS, Spencer SE, Hoofnagle AN, MacCoss MJ bioRxiv : the preprint server for biology 2024 Aug PubMed | DOI

The kinesin motor Kif9 regulates centriolar satellite positioning and mitotic progression Vicente JJ, Wagenbach M, Decarreau J, Zelter A, MacCoss MJ, Davis TN, Wordeman L bioRxiv : the preprint server for biology 2024 Apr PubMed | DOI

Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome Wu CC, Tsantilas KA, Park J, Plubell D, Sanders JA, Naicker P, Govender I, Buthelezi S, Stoychev S, Jordaan J, Merrihew G, Huang E, Parker ED, Riffle M, Hoofnagle AN, Noble WS, Poston KL, Montine TJ, MacCoss MJ bioRxiv : the preprint server for biology 2024 Apr PubMed | DOI

Interlaboratory Comparison of Antibody-Free LC-MS/MS Measurements of C-peptide and Insulin Moradian A, Goonatilleke E, Lin TT, Hatten-Beck M, Emrick M, Schepmoes AA, Fillmore TL, MacCoss MJ, Sechi S, Sobhani K, Little R, Kabytaev K, van Eyk JE, Qian WJ, Hoofnagle AN Clinical chemistry 2024 Jun;70(6):855-864 PubMed | DOI

MBNL1 Regulates Programmed Postnatal Switching Between Regenerative and Differentiated Cardiac States Bailey LRJ, Bugg D, Reichardt IM, Ortaç CD, Nagle A, Gunaje J, Martinson A, Johnson R, MacCoss MJ, Sakamoto T, Kelly DP, Regnier M, Davis J Circulation 2024 Jun;149(23):1812-1829 PubMed | DOI

Longitudinal Transcriptomic, Proteomic, and Metabolomic Response of Citrus sinensis to Diaphorina citri Inoculation of Candidatus Liberibacter asiaticus Lombardi RL, Ramsey JS, Mahoney JE, MacCoss MJ, Heck ML, Slupsky CM Journal of proteome research 2024 Aug;23(8):2857-2869 PubMed | DOI

Hippocampus Glutathione S Reductase Potentially Confers Genetic Resilience to Cognitive Decline in the AD-BXD Mouse Population Saul MC, Litkowski EM, Hadad N, Dunn AR, Boas SM, Wilcox JAL, Robbins JE, Wu Y, Philip VM, Merrihew GE, Park J, De Jager PL, Bridges DE, Menon V, Bennett DA, Hohman TJ, MacCoss MJ, Kaczorowski CC bioRxiv : the preprint server for biology 2024 Jan PubMed | DOI

De novo design of high-affinity binders of bioactive helical peptides Vázquez Torres S, Leung PJY, Venkatesh P, Lutz ID, Hink F, Huynh HH, Becker J, Yeh AH, Juergens D, Bennett NR, Hoofnagle AN, Huang E, MacCoss MJ, Expòsit M, Lee GR, Bera AK, Kang A, De La Cruz J, Levine PM, Li X, Lamb M, Gerben SR, Murray A, Heine P, Korkmaz EN, Nivala J, Stewart L, Watson JL, Rogers JM, Baker D Nature 2024 Feb;626(7998):435-442 PubMed | DOI

2023

Understanding the molecular basis of resilience to Alzheimer’s disease Montine KS, Berson E, Phongpreecha T, Huang Z, Aghaeepour N, Zou JY, MacCoss MJ, Montine TJ Frontiers in neuroscience 2023;17:1311157 PubMed | DOI

Human cerebrospinal fluid single exosomes in Parkinson’s and Alzheimer’s diseases Yakabi K, Berson E, Montine KS, Bendall SC, MacCoss MJ, Poston KL, Montine TJ bioRxiv : the preprint server for biology 2023 Dec PubMed | DOI

Skeletal muscle TFEB signaling promotes central nervous system function and reduces neuroinflammation during aging and neurodegenerative disease Matthews I, Birnbaum A, Gromova A, Huang AW, Liu K, Liu EA, Coutinho K, McGraw M, Patterson DC, Banks MT, Nobles AC, Nguyen N, Merrihew GE, Wang L, Baeuerle E, Fernandez E, Musi N, MacCoss MJ, Miranda HC, La Spada AR, Cortes CJ Cell reports 2023 Nov;42(11):113436 PubMed | DOI

METLIN-CCS: an ion mobility spectrometry collision cross section database Baker ES, Hoang C, Uritboonthai W, Heyman HM, Pratt B, MacCoss M, MacLean B, Plumb R, Aisporna A, Siuzdak G Nature methods 2023 Dec;20(12):1836-1837 PubMed | DOI

Unveiling Resilience to Alzheimer’s Disease: Insights From Brain Regional Proteomic Markers Huang Z, Merrihew GE, Larson EB, Park J, Plubell D, Fox EJ, Montine KS, Keene CD, Latimer CS, Zou JY, MacCoss MJ, Montine TJ Neuroscience insights 2023;18:26331055231201600 PubMed | DOI

Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data-Independent Acquisition 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 Journal of proteome research 2023 Oct;22(10):3290-3300 PubMed | DOI

Proteogenomic data and resources for pan-cancer analysis Li Y, Dou Y, Da Veiga Leprevost F, Geffen Y, Calinawan AP, Aguet F, Akiyama Y, Anand S, Birger C, Cao S, Chaudhary R, Chilappagari P, Cieslik M, Colaprico A, Zhou DC, Day C, Domagalski MJ, Esai Selvan M, Fenyö D, Foltz SM, Francis A, Gonzalez-Robles T, Gümüş ZH, Heiman D, Holck M, Hong R, Hu Y, Jaehnig EJ, Ji J, Jiang W, Katsnelson L, Ketchum KA, Klein RJ, Lei JT, Liang WW, Liao Y, Lindgren CM, Ma W, Ma L, MacCoss MJ, Martins Rodrigues F, McKerrow W, Nguyen N, Oldroyd R, Pilozzi A, Pugliese P, Reva B, Rudnick P, Ruggles KV, Rykunov D, Savage SR, Schnaubelt M, Schraink T, Shi Z, Singhal D, Song X, Storrs E, Terekhanova NV, Thangudu RR, Thiagarajan M, Wang LB, Wang JM, Wang Y, Wen B, Wu Y, Wyczalkowski MA, Xin Y, Yao L, Yi X, Zhang H, Zhang Q, Zuhl M, Getz G, Ding L, Nesvizhskii AI, Wang P, Robles AI, Zhang B, Payne SH Cancer cell 2023 Aug;41(8):1397-1406 PubMed | DOI

Dynamic Data-Independent Acquisition Mass Spectrometry with Real-Time Retrospective Alignment Heil LR, Remes PM, Canterbury JD, Yip P, Barshop WD, Wu CC, MacCoss MJ Analytical chemistry 2023 Aug;95(32):11854-11858 PubMed | DOI

The mitochondrially targeted peptide elamipretide (SS-31) improves ADP sensitivity in aged mitochondria by increasing uptake through the adenine nucleotide translocator (ANT) Pharaoh G, Kamat V, Kannan S, Stuppard RS, Whitson J, Martín-Pérez M, Qian WJ, MacCoss MJ, Villén J, Rabinovitch P, Campbell MD, Sweet IR, Marcinek DJ GeroScience 2023 Dec;45(6):3529-3548 PubMed | DOI

Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data Independent Acquisition 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 bioRxiv : the preprint server for biology 2023 Aug PubMed | DOI

Metrologically Traceable Quantification of 3 Apolipoprotein E Isoforms in Cerebrospinal Fluid Huynh HH, Kuch K, Orquillas A, Forrest K, Barahona-Carrillo L, Keene D, Henderson VW, Wagner AD, Poston KL, Montine TJ, Lin A, Tian L, MacCoss MJ, Emrick MA, Hoofnagle AN Clinical chemistry 2023 Jul;69(7):734-745 PubMed | DOI

Brain proteomic analysis implicates actin filament processes and injury response in resilience to Alzheimer’s disease Huang Z, Merrihew GE, Larson EB, Park J, Plubell D, Fox EJ, Montine KS, Latimer CS, Dirk Keene C, Zou JY, MacCoss MJ, Montine TJ Nature communications 2023 May;14(1):2747 PubMed | DOI

A peptide-centric quantitative proteomics dataset for the phenotypic assessment of Alzheimer’s disease 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 Scientific data 2023 Apr;10(1):206 PubMed | DOI

MBNL1 regulates programmed postnatal switching between regenerative and differentiated cardiac states Bailey LRJ, Bugg D, Reichardt IM, Ortaç CD, Gunaje J, Johnson R, MacCoss MJ, Sakamoto T, Kelly DP, Regnier M, Davis JM bioRxiv : the preprint server for biology 2023 Mar PubMed | DOI

Sampling the proteome by emerging single-molecule and mass spectrometry methods MacCoss MJ, Alfaro JA, Faivre DA, Wu CC, Wanunu M, Slavov N Nature methods 2023 Mar;20(3):339-346 PubMed | DOI

Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments Gatto L, Aebersold R, Cox J, Demichev V, Derks J, Emmott E, Franks AM, Ivanov AR, Kelly RT, Khoury L, Leduc A, MacCoss MJ, Nemes P, Perlman DH, Petelski AA, Rose CM, Schoof EM, Van Eyk J, Vanderaa C, Yates JR, Slavov N Nature methods 2023 Mar;20(3):375-386 PubMed | DOI

Elamipretide Improves ADP Sensitivity in Aged Mitochondria by Increasing Uptake through the Adenine Nucleotide Translocator (ANT) Pharaoh G, Kamat V, Kannan S, Stuppard RS, Whitson J, Martin-Perez M, Qian WJ, MacCoss MJ, Villen J, Rabinovitch P, Campbell MD, Sweet IR, Marcinek DJ bioRxiv : the preprint server for biology 2023 Feb PubMed | DOI

Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline Hoopmann MR, Shteynberg DD, Zelter A, Riffle M, Lyon AS, Agard DA, Luan Q, Nolen BJ, MacCoss MJ, Davis TN, Moritz RL Journal of proteome research 2023 Feb;22(2):647-655 PubMed | DOI

Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins 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 Cell metabolism 2023 Jan;35(1):166-183.e11 PubMed | DOI

The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data Kertesz-Farkas A, Nii Adoquaye Acquaye FL, Bhimani K, Eng JK, Fondrie WE, Grant C, Hoopmann MR, Lin A, Lu YY, Moritz RL, MacCoss MJ, Noble WS Journal of proteome research 2023 Feb;22(2):561-569 PubMed | DOI

The ProteomeXchange consortium at 10 years: 2023 update Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver JJ, Mendoza L, Kundu DJ, Wang S, Bandla C, Kamatchinathan S, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA Nucleic acids research 2023 Jan;51(D1):D1539-D1548 PubMed | DOI

TurnoveR: A Skyline External Tool for Analysis of Protein Turnover in Metabolic Labeling Studies Basisty N, Shulman N, Wehrfritz C, Marsh AN, Shah S, Rose J, Ebert S, Miller M, Dai DF, Rabinovitch PS, Adams CM, MacCoss MJ, MacLean B, Schilling B Journal of proteome research 2023 Feb;22(2):311-322 PubMed | DOI

2022

Elamipretide effects on the skeletal muscle phosphoproteome in aged female mice Campbell MD, Martín-Pérez M, Egertson JD, Gaffrey MJ, Wang L, Bammler T, Rabinovitch PS, MacCoss M, Qian WJ, Villen J, Marcinek D GeroScience 2022 Dec;44(6):2913-2924 PubMed | DOI

Serum plays an important role in reprogramming the seasonal transcriptional profile of brown bear adipocytes Saxton MW, Perry BW, Evans Hutzenbiler BD, Trojahn S, Gee A, Brown AP, Merrihew GE, Park J, Cornejo OE, MacCoss MJ, Robbins CT, Jansen HT, Kelley JL iScience 2022 Oct;25(10):105084 PubMed | DOI

A Targeted Liquid Chromatography-Tandem Mass Spectrometry Method for Simultaneous Quantification of Peptides from the Carboxyl-terminal Region of Type III Procollagen, Biomarkers of Collagen Turnover Huynh HH, Forrest K, Becker JO, Emrick MA, Miller GD, Moncrieffe D, Cowan DA, Thomas A, Thevis M, MacCoss MJ, Hoffstrom B, Byers PH, Eichner D, Hoofnagle AN Clinical chemistry 2022 Oct;68(10):1281-1291 PubMed | DOI

Utilizing Skyline to analyze lipidomics data containing liquid chromatography, ion mobility spectrometry and mass spectrometry dimensions Kirkwood KI, Pratt BS, Shulman N, Tamura K, MacCoss MJ, MacLean BX, Baker ES Nature protocols 2022 Nov;17(11):2415-2430 PubMed | DOI

A male steroid controls female sexual behaviour in the malaria mosquito Peng D, Kakani EG, Mameli E, Vidoudez C, Mitchell SN, Merrihew GE, MacCoss MJ, Adams K, Rinvee TA, Shaw WR, Catteruccia F Nature 2022 Aug;608(7921):93-97 PubMed | DOI

Multiplexed quantification of insulin and C-peptide by LC-MS/MS without the use of antibodies Foulon N, Goonatilleke E, MacCoss MJ, Emrick MA, Hoofnagle AN Journal of mass spectrometry and advances in the clinical lab 2022 Aug;25:19-26 PubMed | DOI

Cullin-independent recognition of HHARI substrates by a dynamic RBR catalytic domain Reiter KH, Zelter A, Janowska MK, Riffle M, Shulman N, MacLean BX, Tamura K, Chambers MC, MacCoss MJ, Davis TN, Guttman M, Brzovic PS, Klevit RE Structure (London, England : 1993) 2022 Sep;30(9):1269-1284.e6 PubMed | DOI

New Views of Old Proteins: Clarifying the Enigmatic Proteome Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Sechi S, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, Kelleher NL Molecular & cellular proteomics : MCP 2022 Jul;21(7):100254 PubMed | DOI

Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data Heil LR, Fondrie WE, McGann CD, Federation AJ, Noble WS, MacCoss MJ, Keich U Journal of proteome research 2022 Jun;21(6):1382-1391 PubMed | DOI

Tandem Mass Spectrometry-Based Amyloid Typing Using Manual Microdissection and Open-Source Data Processing Phipps WS, Smith KD, Yang HY, Henderson CM, Pflaum H, Lerch ML, Fondrie WE, Emrick MA, Wu CC, MacCoss MJ, Noble WS, Hoofnagle AN American journal of clinical pathology 2022 May;157(5):748-757 PubMed | DOI

Age-related disruption of the proteome and acetylome in mouse hearts is associated with loss of function and attenuated by elamipretide (SS-31) and nicotinamide mononucleotide (NMN) treatment Whitson JA, Johnson R, Wang L, Bammler TK, Imai SI, Zhang H, Fredrickson J, Latorre-Esteves E, Bitto A, MacCoss MJ, Rabinovitch PS GeroScience 2022 Jun;44(3):1621-1639 PubMed | DOI

Mitochondrial Inorganic Polyphosphate (polyP) Is a Potent Regulator of Mammalian Bioenergetics in SH-SY5Y Cells: A Proteomics and Metabolomics Study Guitart-Mampel M, Urquiza P, Carnevale Neto F, Anderson JR, Hambardikar V, Scoma ER, Merrihew GE, Wang L, MacCoss MJ, Raftery D, Peffers MJ, Solesio ME Frontiers in cell and developmental biology 2022;10:833127 PubMed | DOI

Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics? Plubell DL, Käll L, Webb-Robertson BJ, Bramer LM, Ives A, Kelleher NL, Smith LM, Montine TJ, Wu CC, MacCoss MJ Journal of proteome research 2022 Apr;21(4):891-898 PubMed | DOI

Activity dependent dissociation of the Homer1 interactome Stillman M, Lautz JD, Johnson RS, MacCoss MJ, Smith SEP Scientific reports 2022 Feb;12(1):3207 PubMed | DOI

Discovery and Visualization of Uncharacterized Drug-Protein Adducts Using Mass Spectrometry Riffle M, Hoopmann MR, Jaschob D, Zhong G, Moritz RL, MacCoss MJ, Davis TN, Isoherranen N, Zelter A Analytical chemistry 2022 Mar;94(8):3501-3509 PubMed | DOI

The metabolome as a biomarker of aging in Drosophila melanogaster Zhao X, Golic FT, Harrison BR, Manoj M, Hoffman EV, Simon N, Johnson R, MacCoss MJ, McIntyre LM, Promislow DEL Aging cell 2022 Feb;21(2):e13548 PubMed | DOI

Skyline Batch: An Intuitive User Interface for Batch Processing with Skyline Marsh AN, Sharma V, Mani SK, Vitek O, MacCoss MJ, MacLean BX Journal of proteome research 2022 Jan;21(1):289-294 PubMed | DOI

Prebiotic Membranes and Micelles Do Not Inhibit Peptide Formation During Dehydration Cohen ZR, Kessenich BL, Hazra A, Nguyen J, Johnson RS, MacCoss MJ, Lalic G, Black RA, Keller SL Chembiochem : a European journal of chemical biology 2022 Feb;23(3):e202100614 PubMed | DOI

Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity Kirkwood KI, Christopher MW, Burgess JL, Littau SR, Foster K, Richey K, Pratt BS, Shulman N, Tamura K, MacCoss MJ, MacLean BX, Baker ES Journal of proteome research 2022 Jan;21(1):232-242 PubMed | DOI

Does Data-Independent Acquisition Data Contain Hidden Gems? A Case Study Related to Alzheimer’s Disease Hubbard EE, Heil LR, Merrihew GE, Chhatwal JP, Farlow MR, McLean CA, Ghetti B, Newell KL, Frosch MP, Bateman RJ, Larson EB, Keene CD, Perrin RJ, Montine TJ, MacCoss MJ, Julian RR Journal of proteome research 2022 Jan;21(1):118-131 PubMed | DOI

Host Plant Adaptation Drives Changes in Diaphorina citri Proteome Regulation, Proteoform Expression, and Transmission of ‘Candidatus Liberibacter asiaticus’, the Citrus Greening Pathogen Ramsey JS, Ammar ED, Mahoney JE, Rivera K, Johnson R, Igwe DO, Thannhauser TW, MacCoss MJ, Hall DG, Heck M Phytopathology 2022 Jan;112(1):101-115 PubMed | DOI

Lysosomal targetomics of ghr KO mice shows chaperone-mediated autophagy degrades nucleocytosolic acetyl-coA enzymes Endicott SJ, Monovich AC, Huang EL, Henry EI, Boynton DN, Beckmann LJ, MacCoss MJ, Miller RA Autophagy 2022 Jul;18(7):1551-1571 PubMed | DOI

2021

Mass spectrometric identification of immunogenic SARS-CoV-2 epitopes and cognate TCRs Pan K, Chiu Y, Huang E, Chen M, Wang J, Lai I, Singh S, Shaw RM, MacCoss MJ, Yee C Proceedings of the National Academy of Sciences of the United States of America 2021 Nov;118(46) PubMed | DOI

De novo design of tyrosine and serine kinase-driven protein switches Woodall NB, Weinberg Z, Park J, Busch F, Johnson RS, Feldbauer MJ, Murphy M, Ahlrichs M, Yousif I, MacCoss MJ, Wysocki VH, El-Samad H, Baker D Nature structural & molecular biology 2021 Sep;28(9):762-770 PubMed | DOI

Elamipretide (SS-31) treatment attenuates age-associated post-translational modifications of heart proteins Whitson JA, Martín-Pérez M, Zhang T, Gaffrey MJ, Merrihew GE, Huang E, White CC, Kavanagh TJ, Qian WJ, Campbell MD, MacCoss MJ, Marcinek DJ, Villén J, Rabinovitch PS GeroScience 2021 Oct;43(5):2395-2412 PubMed | DOI

Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds Dele-Oni DO, Christianson KE, Egri SB, Vaca Jacome AS, DeRuff KC, Mullahoo J, Sharma V, Davison D, Ko T, Bula M, Blanchard J, Young JZ, Litichevskiy L, Lu X, Lam D, Asiedu JK, Toder C, Officer A, Peckner R, MacCoss MJ, Tsai LH, Carr SA, Papanastasiou M, Jaffe JD Scientific data 2021 Aug;8(1):226 PubMed | DOI

Comparison of Unit Resolution Versus High-Resolution Accurate Mass for Parallel Reaction Monitoring Heil LR, Remes PM, MacCoss MJ Journal of proteome research 2021 Sep;20(9):4435-4442 PubMed | DOI

Immunogenic SARS-CoV2 Epitopes Defined by Mass Spectrometry Pan K, Chiu Y, Huang E, Chen M, Wang J, Lai I, Singh S, Shaw R, MacCoss M, Yee C bioRxiv : the preprint server for biology 2021 Jul PubMed | DOI

Identification of Actin Filament-Associated Proteins in Giardia lamblia Steele-Ogus MC, Johnson RS, MacCoss MJ, Paredez AR Microbiology spectrum 2021 Sep;9(1):e0055821 PubMed | DOI

University of Washington Nathan Shock Center: innovation to advance aging research Kaeberlein M, Bitto A, Dunham MJ, Ladiges W, Lee SI, MacCoss MJ, Mendenhall A, Promislow DEL, Rabinovitch PS, Villén J, Wang L, Wang Y, Young JE GeroScience 2021 Oct;43(5):2161-2165 PubMed | DOI

Proteomics support the threespine stickleback egg coat as a protective oocyte envelope Killingbeck EE, Wilburn DB, Merrihew GE, MacCoss MJ, Swanson WJ Molecular reproduction and development 2021 Jul;88(7):500-515 PubMed | DOI

Affinity Purification-Mass Spectrometry Identifies a Novel Interaction between a Polerovirus and a Conserved Innate Immunity Aphid Protein that Regulates Transmission Efficiency DeBlasio SL, Wilson JR, Tamborindeguy C, Johnson RS, Pinheiro PV, MacCoss MJ, Gray SM, Heck M Journal of proteome research 2021 Jun;20(6):3365-3387 PubMed | DOI

Staging Encystation Progression in Giardia lamblia Using Encystation-Specific Vesicle Morphology and Associating Molecular Markers Thomas EB, Sutanto R, Johnson RS, Shih HW, Alas GCM, Krtková J, MacCoss MJ, Paredez AR Frontiers in cell and developmental biology 2021;9:662945 PubMed | DOI

CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation Brilot AF, Lyon AS, Zelter A, Viswanath S, Maxwell A, MacCoss MJ, Muller EG, Sali A, Davis TN, Agard DA eLife 2021 May;10 PubMed | DOI

Slowed Protein Turnover in Aging Drosophila Reflects a Shift in Cellular Priorities Vincow ES, Thomas RE, Merrihew GE, MacCoss MJ, Pallanck LJ The journals of gerontology. Series A, Biological sciences and medical sciences 2021 Sep;76(10):1734-1739 PubMed | DOI

2020

Avant-garde: an automated data-driven DIA data curation tool Vaca Jacome AS, Peckner R, Shulman N, Krug K, DeRuff KC, Officer A, Christianson KE, MacLean B, MacCoss MJ, Carr SA, Jaffe JD Nature methods 2020 Dec;17(12):1237-1244 PubMed | DOI

A proteomic approach reveals possible molecular mechanisms and roles for endosymbiotic bacteria in begomovirus transmission by whiteflies Kliot A, Johnson RS, MacCoss MJ, Kontsedalov S, Lebedev G, Czosnek H, Heck M, Ghanim M GigaScience 2020 Nov;9(11) PubMed | DOI

Development on Citrus medica infected with ‘Candidatus Liberibacter asiaticus’ has sex-specific and -nonspecific impacts on adult Diaphorina citri and its endosymbionts Coates LC, Mahoney J, Ramsey JS, Warwick E, Johnson R, MacCoss MJ, Krasnoff SB, Howe KJ, Moulton K, Saha S, Mueller LA, Hall DG, Shatters RG, Heck ML, Slupsky CM PloS one 2020;15(10):e0239771 PubMed | DOI

Acarbose has sex-dependent and -independent effects on age-related physical function, cardiac health, and lipid biology Herrera JJ, Louzon S, Pifer K, Leander D, Merrihew GE, Park JH, Szczesniak K, Whitson J, Wilkinson JE, Fiehn O, MacCoss MJ, Day SM, Miller RA, Garratt M JCI insight 2020 Nov;5(21) PubMed | DOI

Highly Multiplex Targeted Proteomics Enabled by Real-Time Chromatographic Alignment Remes PM, Yip P, MacCoss MJ Analytical chemistry 2020 Sep;92(17):11809-11817 PubMed | DOI

Late-life restoration of mitochondrial function reverses cardiac dysfunction in old mice Chiao YA, Zhang H, Sweetwyne M, Whitson J, Ting YS, Basisty N, Pino LK, Quarles E, Nguyen NH, Campbell MD, Zhang T, Gaffrey MJ, Merrihew G, Wang L, Yue Y, Duan D, Granzier HL, Szeto HH, Qian WJ, Marcinek D, MacCoss MJ, Rabinovitch P eLife 2020 Jul;9 PubMed | DOI

RNA aptamer capture of macromolecular complexes for mass spectrometry analysis Ray J, Kruse A, Ozer A, Kajitani T, Johnson R, MacCoss M, Heck M, Lis JT Nucleic acids research 2020 Sep;48(15):e90 PubMed | DOI

Composition of Caenorhabditis elegans extracellular vesicles suggests roles in metabolism, immunity, and aging Russell JC, Kim TK, Noori A, Merrihew GE, Robbins JE, Golubeva A, Wang K, MacCoss MJ, Kaeberlein M GeroScience 2020 Aug;42(4):1133-1145 PubMed | DOI

piNET: a versatile web platform for downstream analysis and visualization of proteomics data Shamsaei B, Chojnacki S, Pilarczyk M, Najafabadi M, Niu W, Chen C, Ross K, Matlock A, Muhlich J, Chutipongtanate S, Zheng J, Turner J, Vidović D, Jaffe J, MacCoss M, Wu C, Pillai A, Ma’ayan A, Schürer S, Kouril M, Medvedovic M, Meller J Nucleic acids research 2020 Jul;48(W1):W85-W93 PubMed | DOI

Audit logs to enforce document integrity in Skyline and Panorama Rohde T, Chupalov R, Shulman N, Sharma V, Eckels J, Pratt BS, MacCoss MJ, MacLean BX Bioinformatics (Oxford, England) 2020 Aug;36(15):4366-4368 PubMed | DOI

Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries Pino LK, Just SC, MacCoss MJ, Searle BC Molecular & cellular proteomics : MCP 2020 Jul;19(7):1088-1103 PubMed | DOI

Highly Parallel Quantification and Compartment Localization of Transcription Factors and Nuclear Proteins Federation AJ, Nandakumar V, Searle BC, Stergachis A, Wang H, Pino LK, Merrihew G, Ting YS, Howard N, Kutyavin T, MacCoss MJ, Stamatoyannopoulos JA Cell reports 2020 Feb;30(8):2463-2471.e5 PubMed | DOI

Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics Pino LK, Searle BC, Yang HY, Hoofnagle AN, Noble WS, MacCoss MJ Journal of proteome research 2020 Mar;19(3):1147-1153 PubMed | DOI

Peptidomics Approaches for the Identification of Bioactive Molecules from Diaphorina citri Fleites LA, Johnson R, Kruse AR, Nachman RJ, Hall DG, MacCoss M, Heck ML Journal of proteome research 2020 Apr;19(4):1392-1408 PubMed | DOI

Mutual Balance of Histone Deacetylases 1 and 2 and the Acetyl Reader ATAD2 Regulates the Level of Acetylation of Histone H4 on Nascent Chromatin of Human Cells Lazarchuk P, Hernandez-Villanueva J, Pavlova MN, Federation A, MacCoss M, Sidorova JM Molecular and cellular biology 2020 Apr;40(9) PubMed | DOI

Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics Adams KJ, Pratt B, Bose N, Dubois LG, St John-Williams L, Perrott KM, Ky K, Kapahi P, Sharma V, MacCoss MJ, Moseley MA, Colton CA, MacLean BX, Schilling B, Thompson JW Journal of proteome research 2020 Apr;19(4):1447-1458 PubMed | DOI

Rapamycin persistently improves cardiac function in aged, male and female mice, even following cessation of treatment Quarles E, Basisty N, Chiao YA, Merrihew G, Gu H, Sweetwyne MT, Fredrickson J, Nguyen NH, Razumova M, Kooiker K, Moussavi-Harami F, Regnier M, Quarles C, MacCoss M, Rabinovitch PS Aging cell 2020 Feb;19(2):e13086 PubMed | DOI

Assessing Protein Sequence Database Suitability Using De Novo Sequencing Johnson RS, Searle BC, Nunn BL, Gilmore JM, Phillips M, Amemiya CT, Heck M, MacCoss MJ Molecular & cellular proteomics : MCP 2020 Jan;19(1):198-208 PubMed | DOI

The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics 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, Hermjakob H, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA Nucleic acids research 2020 Jan;48(D1):D1145-D1152 PubMed | DOI

The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics Pino LK, Searle BC, Bollinger JG, Nunn B, MacLean B, MacCoss MJ Mass spectrometry reviews 2020 May;39(3):229-244 PubMed | DOI

2019

Differential effects of various genetic mouse models of the mechanistic target of rapamycin complex I inhibition on heart failure Dai DF, Liu Y, Basisty N, Karunadharma P, Dastidar SG, Chiao YA, Chen T, Beyer RP, Chin MT, Maccoss M, La Spada AR, Rabinovitch PS GeroScience 2019 Dec;41(6):847-860 PubMed | DOI

Kinetochore-associated Stu2 promotes chromosome biorientation in vivo Miller MP, Evans RK, Zelter A, Geyer EA, MacCoss MJ, Rice LM, Davis TN, Asbury CL, Biggins S PLoS genetics 2019 Oct;15(10):e1008423 PubMed | DOI

Thesaurus: quantifying phosphopeptide positional isomers Searle BC, Lawrence RT, MacCoss MJ, Villén J Nature methods 2019 Aug;16(8):703-706 PubMed | DOI

First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O’Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A Analytical chemistry 2019 Jun;91(11):6953-6961 PubMed | DOI

Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective Vincow ES, Thomas RE, Merrihew GE, Shulman NJ, Bammler TK, MacDonald JW, MacCoss MJ, Pallanck LJ Autophagy 2019 Sep;15(9):1592-1605 PubMed | DOI

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 Journal of the American Society for Mass Spectrometry 2019 Apr;30(4):669-684 PubMed | DOI

Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL Molecular & cellular proteomics : MCP 2019 Jan;18(1):1-2 PubMed | DOI

Improving mitochondrial function with SS-31 reverses age-related redox stress and improves exercise tolerance in aged mice Campbell MD, Duan J, Samuelson AT, Gaffrey MJ, Merrihew GE, Egertson JD, Wang L, Bammler TK, Moore RJ, White CC, Kavanagh TJ, Voss JG, Szeto HH, Rabinovitch PS, MacCoss MJ, Qian WJ, Marcinek DJ Free radical biology & medicine 2019 Apr;134:268-281 PubMed | DOI

Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis Krahmer J, Goralogia GS, Kubota A, Zardilis A, Johnson RS, Song YH, MacCoss MJ, Le Bihan T, Halliday KJ, Imaizumi T, Millar AJ FEBS letters 2019 Feb;593(3):319-338 PubMed | DOI

Data-Independent Acquisition Mass Spectrometry To Quantify Protein Levels in FFPE Tumor Biopsies for Molecular Diagnostics Kim YJ, Sweet SMM, Egertson JD, Sedgewick AJ, Woo S, Liao WL, Merrihew GE, Searle BC, Vaske C, Heaton R, MacCoss MJ, Hembrough T Journal of proteome research 2019 Jan;18(1):426-435 PubMed | DOI

2018

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 Nature communications 2018 Dec;9(1):5128 PubMed | DOI

The Interaction Dynamics of Two Potato Leafroll Virus Movement Proteins Affects Their Localization to the Outer Membranes of Mitochondria and Plastids DeBlasio SL, Xu Y, Johnson RS, Rebelo AR, MacCoss MJ, Gray SM, Heck M Viruses 2018 Oct;10(11) PubMed | DOI

Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories Pino LK, Searle BC, Huang EL, Noble WS, Hoofnagle AN, MacCoss MJ Analytical chemistry 2018 Nov;90(21):13112-13117 PubMed | DOI

Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles Thomas RE, Vincow ES, Merrihew GE, MacCoss MJ, Davis MY, Pallanck LJ PLoS genetics 2018 Sep;14(9):e1007694 PubMed | DOI

Candidatus Liberibacter asiaticus Minimally Alters Expression of Immunity and Metabolism Proteins in Hemolymph of Diaphorina citri, the Insect Vector of Huanglongbing Kruse A, Ramsey JS, Johnson R, Hall DG, MacCoss MJ, Heck M Journal of proteome research 2018 Sep;17(9):2995-3011 PubMed | DOI

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 Journal of the American Society for Mass Spectrometry 2018 Nov;29(11):2182-2188 PubMed | DOI

Quantitative evolutionary proteomics of seminal fluid from primates with different mating systems Claw KG, George RD, MacCoss MJ, Swanson WJ BMC genomics 2018 Jun;19(1):488 PubMed | DOI

Novel phosphorylation states of the yeast spindle pole body Fong KK, Zelter A, Graczyk B, Hoyt JM, Riffle M, Johnson R, MacCoss MJ, Davis TN Biology open 2018 Oct;7(10) PubMed | DOI

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 systems 2018 Apr;6(4):424-443.e7 PubMed | DOI

A Biofilm Matrix-Associated Protease Inhibitor Protects Pseudomonas aeruginosa from Proteolytic Attack Tseng BS, Reichhardt C, Merrihew GE, Araujo-Hernandez SA, Harrison JJ, MacCoss MJ, Parsek MR mBio 2018 Apr;9(2) PubMed | DOI

Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics Peckner R, Myers SA, Jacome ASV, Egertson JD, Abelin JG, MacCoss MJ, Carr SA, Jaffe JD Nature methods 2018 May;15(5):371-378 PubMed | DOI

A Stem-Loop Structure in Potato Leafroll Virus Open Reading Frame 5 (ORF5) Is Essential for Readthrough Translation of the Coat Protein ORF Stop Codon 700 Bases Upstream Xu Y, Ju HJ, DeBlasio S, Carino EJ, Johnson R, MacCoss MJ, Heck M, Miller WA, Gray SM Journal of virology 2018 Jun;92(11) PubMed | DOI

Human Ska complex and Ndc80 complex interact to form a load-bearing assembly that strengthens kinetochore-microtubule attachments Helgeson LA, Zelter A, Riffle M, MacCoss MJ, Asbury CL, Davis TN Proceedings of the National Academy of Sciences of the United States of America 2018 Mar;115(11):2740-2745 PubMed | DOI

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 Molecular & cellular proteomics : MCP 2018 Jun;17(6):1239-1244 PubMed | DOI

How many human proteoforms are there? Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B Nature chemical biology 2018 Feb;14(3):206-214 PubMed | DOI

Nonlinear Regression Improves Accuracy of Characterization of Multiplexed Mass Spectrometric Assays Galitzine C, Egertson JD, Abbatiello S, Henderson CM, Pino LK, MacCoss M, Hoofnagle AN, Vitek O Molecular & cellular proteomics : MCP 2018 May;17(5):913-924 PubMed | DOI

Identification of Wiskott-Aldrich syndrome protein (WASP) binding sites on the branched actin filament nucleator Arp2/3 complex Luan Q, Zelter A, MacCoss MJ, Davis TN, Nolen BJ Proceedings of the National Academy of Sciences of the United States of America 2018 Feb;115(7):E1409-E1418 PubMed | DOI

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 Clinical chemistry 2018 Feb;64(2):408-410 PubMed | DOI

DnaJ Homolog Subfamily B Member 9 Is a Putative Autoantigen in Fibrillary GN Andeen NK, Yang HY, Dai DF, MacCoss MJ, Smith KD Journal of the American Society of Nephrology : JASN 2018 Jan;29(1):231-239 PubMed | DOI

Stable Isotope Labeling Reveals Novel Insights Into Ubiquitin-Mediated Protein Aggregation With Age, Calorie Restriction, and Rapamycin Treatment Basisty NB, Liu Y, Reynolds J, Karunadharma PP, Dai DF, Fredrickson J, Beyer RP, MacCoss MJ, Rabinovitch PS The journals of gerontology. Series A, Biological sciences and medical sciences 2018 Apr;73(5):561-570 PubMed | DOI

2017

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 Nature methods 2017 Sep;14(9):921-927 PubMed | DOI

Evaluation of a Bead-Free Coimmunoprecipitation Technique for Identification of Virus-Host Protein Interactions Using High-Resolution Mass Spectrometry DeBlasio SL, Bereman MS, Mahoney J, Thannhauser TW, Gray SM, MacCoss MJ, Cilia Heck M Journal of biomolecular techniques : JBT 2017 Sep;28(3):111-121 PubMed | DOI

PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data Ting YS, Egertson JD, Bollinger JG, Searle BC, Payne SH, Noble WS, MacCoss MJ Nature methods 2017 Sep;14(9):903-908 PubMed | DOI

Development of Selected Reaction Monitoring Methods to Systematically Quantify Kinase Abundance and Phosphorylation Stoichiometry in Human Samples Beck K, Camp N, Bereman M, Bollinger J, Egertson J, MacCoss M, Wolf-Yadlin A Methods in molecular biology (Clifton, N.J.) 2017;1636:353-369 PubMed | DOI

A mass spectrometry-based proteomic analysis of Homer2-interacting proteins in the mouse brain Goulding SP, Szumlinski KK, Contet C, MacCoss MJ, Wu CC Journal of proteomics 2017 Aug;166:127-137 PubMed | DOI

Proteomic analyses of nucleus laminaris identified candidate targets of the fragile X mental retardation protein Sakano H, Zorio DAR, Wang X, Ting YS, Noble WS, MacCoss MJ, Rubel EW, Wang Y The Journal of comparative neurology 2017 Oct;525(15):3341-3359 PubMed | DOI

Combining ‘omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut Kruse A, Fattah-Hosseini S, Saha S, Johnson R, Warwick E, Sturgeon K, Mueller L, MacCoss MJ, Shatters RG, Cilia Heck M PloS one 2017;12(6):e0179531 PubMed | DOI

TCP4-dependent induction of CONSTANS transcription requires GIGANTEA in photoperiodic flowering in Arabidopsis Kubota A, Ito S, Shim JS, Johnson RS, Song YH, Breton G, Goralogia GS, Kwon MS, Laboy Cintrón D, Koyama T, Ohme-Takagi M, Pruneda-Paz JL, Kay SA, MacCoss MJ, Imaizumi T PLoS genetics 2017 Jun;13(6):e1006856 PubMed | DOI

Proteomics Analysis Identifies Orthologs of Human Chitinase-Like Proteins as Inducers of Tube Morphogenesis Defects in Drosophila melanogaster Zimmerman SG, Merrihew GE, MacCoss MJ, Berg CA Genetics 2017 Jun;206(2):973-984 PubMed | DOI

Automated Trapping Column Exchanger for High-Throughput Nanoflow Liquid Chromatography Spencer SE, Corso TN, Bollinger JG, Henderson CM, Hoofnagle AN, MacCoss MJ Analytical chemistry 2017 Feb;89(4):2383-2389 PubMed | DOI

The Ndc80 complex bridges two Dam1 complex rings Kim JO, Zelter A, Umbreit NT, Bollozos A, Riffle M, Johnson R, MacCoss MJ, Asbury CL, Davis TN eLife 2017 Feb;6 PubMed | DOI

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 Molecular & cellular proteomics : MCP 2017 Mar;16(3):327-328 PubMed | DOI

Quantification by nano liquid chromatography parallel reaction monitoring mass spectrometry of human apolipoprotein A-I, apolipoprotein B, and hemoglobin A1c in dried blood spots Henderson CM, Bollinger JG, Becker JO, Wallace JM, Laha TJ, MacCoss MJ, Hoofnagle AN Proteomics. Clinical applications 2017 Jul;11(7-8) PubMed | DOI

2016

Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer 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, Stoddard BL, Fairlie WD, Hockenbery DM, Baker D eLife 2016 Nov;5 PubMed | DOI

Model System-Guided Protein Interaction Mapping for Virus Isolated from Phloem Tissue DeBlasio SL, Johnson RS, MacCoss MJ, Gray SM, Cilia M Journal of proteome research 2016 Dec;15(12):4601-4611 PubMed | DOI

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 Journal of proteome research 2016 Dec;15(12):4763-4769 PubMed | DOI

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0 The M, MacCoss MJ, Noble WS, Käll L Journal of the American Society for Mass Spectrometry 2016 Nov;27(11):1719-1727 PubMed | DOI

Staphylococcus aureus Protein A Mediates Interspecies Interactions at the Cell Surface of Pseudomonas aeruginosa Armbruster CR, Wolter DJ, Mishra M, Hayden HS, Radey MC, Merrihew G, MacCoss MJ, Burns J, Wozniak DJ, Parsek MR, Hoffman LR mBio 2016 May;7(3) PubMed | DOI

The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles Topalidou I, Cattin-Ortolá J, Pappas AL, Cooper K, Merrihew GE, MacCoss MJ, Ailion M PLoS genetics 2016 May;12(5):e1006074 PubMed | DOI

Mitochondrial-targeted catalase is good for the old mouse proteome, but not for the young: ‘reverse’ antagonistic pleiotropy? Basisty N, Dai DF, Gagnidze A, Gitari L, Fredrickson J, Maina Y, Beyer RP, Emond MJ, Hsieh EJ, MacCoss MJ, Martin GM, Rabinovitch PS Aging cell 2016 Aug;15(4):634-45 PubMed | DOI

Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A Journal of structural biology 2016 Jun;194(3):303-10 PubMed | DOI

Rapamycin transiently induces mitochondrial remodeling to reprogram energy metabolism in old hearts Chiao YA, Kolwicz SC, Basisty N, Gagnidze A, Zhang J, Gu H, Djukovic D, Beyer RP, Raftery D, MacCoss M, Tian R, Rabinovitch PS Aging 2016 Feb;8(2):314-27 PubMed | DOI

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 in molecular biology (Clifton, N.J.) 2016;1410:223-36 PubMed | DOI

Selecting Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as Analytical Standards Bollinger JG, Stergachis AB, Johnson RS, Egertson JD, MacCoss MJ Methods in molecular biology (Clifton, N.J.) 2016;1410:207-21 PubMed | DOI

A targeted proteomic strategy for the measurement of oral cancer candidate biomarkers in human saliva Kawahara R, Bollinger JG, Rivera C, Ribeiro AC, Brandão TB, Paes Leme AF, MacCoss MJ Proteomics 2016 Jan;16(1):159-73 PubMed | DOI

Age modifies respiratory complex I and protein homeostasis in a muscle type-specific manner Kruse SE, Karunadharma PP, Basisty N, Johnson R, Beyer RP, MacCoss MJ, Rabinovitch PS, Marcinek DJ Aging cell 2016 Feb;15(1):89-99 PubMed | DOI

2015

Metabolic Interplay between the Asian Citrus Psyllid and Its Profftella Symbiont: An Achilles’ Heel of the Citrus Greening Insect Vector Ramsey JS, Johnson RS, Hoki JS, Kruse A, Mahoney J, Hilf ME, Hunter WB, Hall DG, Schroeder FC, MacCoss MJ, Cilia M PloS one 2015;10(11):e0140826 PubMed | DOI

The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling Zelter A, Bonomi M, Kim JO, Umbreit NT, Hoopmann MR, Johnson R, Riffle M, Jaschob D, MacCoss MJ, Moritz RL, Davis TN Nature communications 2015 Nov;6:8673 PubMed | DOI

Regulation of outer kinetochore Ndc80 complex-based microtubule attachments by the central kinetochore Mis12/MIND complex Kudalkar EM, Scarborough EA, Umbreit NT, Zelter A, Gestaut DR, Riffle M, Johnson RS, MacCoss MJ, Asbury CL, Davis TN Proceedings of the National Academy of Sciences of the United States of America 2015 Oct;112(41):E5583-9 PubMed | DOI

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 Analytical chemistry 2015 Oct;87(20):10222-9 PubMed | DOI

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 Molecular & cellular proteomics : MCP 2015 Sep;14(9):2301-7 PubMed | DOI

Visualization and dissemination of multidimensional proteomics data comparing protein abundance during Caenorhabditis elegans development Riffle M, Merrihew GE, Jaschob D, Sharma V, Davis TN, Noble WS, MacCoss MJ Journal of the American Society for Mass Spectrometry 2015 Nov;26(11):1827-36 PubMed | DOI

A deeper look into Comet–implementation and features Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ Journal of the American Society for Mass Spectrometry 2015 Nov;26(11):1865-74 PubMed | DOI

Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments Searle BC, Egertson JD, Bollinger JG, Stergachis AB, MacCoss MJ Molecular & cellular proteomics : MCP 2015 Sep;14(9):2331-40 PubMed | DOI

Multiplexed peptide analysis using data-independent acquisition and Skyline Egertson JD, MacLean B, Johnson R, Xuan Y, MacCoss MJ Nature protocols 2015 Jun;10(6):887-903 PubMed | DOI

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 Molecular & cellular proteomics : MCP 2015 Sep;14(9):2405-19 PubMed | DOI

Respiratory chain protein turnover rates in mice are highly heterogeneous but strikingly conserved across tissues, ages, and treatments Karunadharma PP, Basisty N, Chiao YA, Dai DF, Drake R, Levy N, Koh WJ, Emond MJ, Kruse S, Marcinek D, Maccoss MJ, Rabinovitch PS FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2015 Aug;29(8):3582-92 PubMed | DOI

Kojak: efficient analysis of chemically cross-linked protein complexes Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL Journal of proteome research 2015 May;14(5):2190-8 PubMed | DOI

Subacute calorie restriction and rapamycin discordantly alter mouse liver proteome homeostasis and reverse aging effects 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 Aging cell 2015 Aug;14(4):547-57 PubMed | DOI

Potato leafroll virus structural proteins manipulate overlapping, yet distinct protein interaction networks during infection DeBlasio SL, Johnson R, Sweeney MM, Karasev A, Gray SM, MacCoss MJ, Cilia M Proteomics 2015 Jun;15(12):2098-112 PubMed | DOI

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 Molecular & cellular proteomics : MCP 2015 Sep;14(9):2357-74 PubMed | DOI

Insights into the polerovirus-plant interactome revealed by coimmunoprecipitation and mass spectrometry DeBlasio SL, Johnson R, Mahoney J, Karasev A, Gray SM, MacCoss MJ, Cilia M Molecular plant-microbe interactions : MPMI 2015 Apr;28(4):467-81 PubMed | DOI

Substrate trapping proteomics reveals targets of the βTrCP2/FBXW11 ubiquitin ligase Kim TY, Siesser PF, Rossman KL, Goldfarb D, Mackinnon K, Yan F, Yi X, MacCoss MJ, Moon RT, Der CJ, Major MB Molecular and cellular biology 2015 Jan;35(1):167-81 PubMed | DOI

2014

Distinct roles of FKF1, Gigantea, and Zeitlupe proteins in the regulation of Constans stability in Arabidopsis photoperiodic flowering Song YH, Estrada DA, Johnson RS, Kim SK, Lee SY, MacCoss MJ, Imaizumi T Proceedings of the National Academy of Sciences of the United States of America 2014 Dec;111(49):17672-7 PubMed | DOI

Human valacyclovir hydrolase/biphenyl hydrolase-like protein is a highly efficient homocysteine thiolactonase Marsillach J, Suzuki SM, Richter RJ, McDonald MG, Rademacher PM, MacCoss MJ, Hsieh EJ, Rettie AE, Furlong CE PloS one 2014;9(10):e110054 PubMed | DOI

Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics Canterbury JD, Merrihew GE, MacCoss MJ, Goodlett DR, Shaffer SA Journal of the American Society for Mass Spectrometry 2014 Dec;25(12):2048-59 PubMed | DOI

Kinetochore biorientation in Saccharomyces cerevisiae requires a tightly folded conformation of the Ndc80 complex Tien JF, Umbreit NT, Zelter A, Riffle M, Hoopmann MR, Johnson RS, Fonslow BR, Yates JR, MacCoss MJ, Moritz RL, Asbury CL, Davis TN Genetics 2014 Dec;198(4):1483-93 PubMed | DOI

Crux: rapid open source protein tandem mass spectrometry analysis 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 Journal of proteome research 2014 Oct;13(10):4488-91 PubMed | DOI

Comparative analysis of the transcriptome across distant species 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, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R Nature 2014 Aug;512(7515):445-8 PubMed | DOI

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 Journal of proteome research 2014 Sep;13(9):4205-10 PubMed | DOI

Hyaluronan enhances wound repair and increases collagen III in aged dermal wounds Damodarasamy M, Johnson RS, Bentov I, MacCoss MJ, Vernon RB, Reed MJ Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society 2014;22(4):521-6 PubMed | DOI

Evidence for lysine acetylation in the coat protein of a polerovirus Cilia M, Johnson R, Sweeney M, DeBlasio SL, Bruce JE, MacCoss MJ, Gray SM The Journal of general virology 2014 Oct;95(Pt 10):2321-2327 PubMed | DOI

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 (Oxford, England) 2014 Sep;30(17):2521-3 PubMed | DOI

Altered proteome turnover and remodeling by short-term caloric restriction or rapamycin rejuvenate the aging heart 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 Aging cell 2014 Jun;13(3):529-39 PubMed | DOI

Evidence of the biochemical basis of host virulence in the greenbug aphid, Schizaphis graminum (Homoptera: Aphididae) Pinheiro P, Bereman MS, Burd J, Pals M, Armstrong S, Howe KJ, Thannhauser TW, MacCoss MJ, Gray SM, Cilia M Journal of proteome research 2014 Apr;13(4):2094-108 PubMed | DOI

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 Journal of the American Society for Mass Spectrometry 2014 Apr;25(4):581-7 PubMed | DOI

Accounting for population variation in targeted proteomics Fujimoto GM, Monroe ME, Rodriguez L, Wu C, MacLean B, Smith RD, MacCoss MJ, Payne SH Journal of proteome research 2014 Jan;13(1):321-3 PubMed | DOI

Maximizing peptide identification events in proteomic workflows using data-dependent acquisition (DDA) Bateman NW, Goulding SP, Shulman NJ, Gadok AK, Szumlinski KK, MacCoss MJ, Wu CC Molecular & cellular proteomics : MCP 2014 Jan;13(1):329-38 PubMed | DOI

Proteogenomic database construction driven from large scale RNA-seq data Woo S, Cha SW, Merrihew G, He Y, Castellana N, Guest C, MacCoss M, Bafna V Journal of proteome research 2014 Jan;13(1):21-8 PubMed | DOI

2013

Selection on plant male function genes identifies candidates for reproductive isolation of yellow monkeyflowers Aagaard JE, George RD, Fishman L, Maccoss MJ, Swanson WJ PLoS genetics 2013;9(12):e1003965 PubMed | DOI

Genomic and proteomic analysis of Schizaphis graminum reveals cyclophilin proteins are involved in the transmission of cereal yellow dwarf virus Tamborindeguy C, Bereman MS, DeBlasio S, Igwe D, Smith DM, White F, MacCoss MJ, Gray SM, Cilia M PloS one 2013;8(8):e71620 PubMed | DOI

Global proteomics and pathway analysis of pressure-overload-induced heart failure and its attenuation by mitochondrial-targeted peptides 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 Circulation. Heart failure 2013 Sep;6(5):1067-76 PubMed | DOI

Molecular mechanisms underlying genotype-dependent responses to dietary restriction 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, Chen W, Yu T, Goswami S, Higgins S, Holmberg M, Jeong KS, Kim JR, Klum S, Liao E, Lin MS, Lo W, Miller H, Olsen B, Peng ZJ, Pollard T, Pradeep P, Pruett D, Rai D, Ros V, Singh M, Spector BL, Vander Wende H, An EH, Fletcher M, Jelic M, Rabinovitch PS, MacCoss MJ, Han JD, Kennedy BK, Kaeberlein M Aging cell 2013 Dec;12(6):1050-61 PubMed | DOI

Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer Conlon KP, Basrur V, Rolland D, Wolfe T, Nesvizhskii AI, MacCoss MJ, Lim MS, Elenitoba-Johnson KS Molecular & cellular proteomics : MCP 2013 Oct;12(10):2714-23 PubMed | DOI

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 Nature methods 2013 Aug;10(8):744-6 PubMed | DOI

Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast 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, Dunham MJ, Maccoss MJ, Akey JM Genome research 2013 Sep;23(9):1496-504 PubMed | DOI

Rapid assessment of RNAi-mediated protein depletion by selected reaction monitoring mass spectrometry Glukhova VA, Tomazela DM, Findlay GD, Monnat RJ, MacCoss MJ Journal of proteome research 2013 Jul;12(7):3246-54 PubMed | DOI

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 Molecular & cellular proteomics : MCP 2013 Sep;12(9):2623-39 PubMed | DOI

Label-free differential analysis of murine postsynaptic densities Goulding SP, Maccoss MJ, Wu CC Methods in molecular biology (Clifton, N.J.) 2013;1002:295-309 PubMed | DOI

Mass spectrometry and next-generation sequencing reveal an abundant and rapidly evolving abalone sperm protein Palmer MR, McDowall MH, Stewart L, Ouaddi A, MacCoss MJ, Swanson WJ Molecular reproduction and development 2013 Jun;80(6):460-5 PubMed | DOI

The PINK1-Parkin pathway promotes both mitophagy and selective respiratory chain turnover in vivo Vincow ES, Merrihew G, Thomas RE, Shulman NJ, Beyer RP, MacCoss MJ, Pallanck LJ Proceedings of the National Academy of Sciences of the United States of America 2013 Apr;110(16):6400-5 PubMed | DOI

Hematopoietic protein-1 regulates the actin membrane skeleton and membrane stability in murine erythrocytes Chan MM, Wooden JM, Tsang M, Gilligan DM, Hirenallur-S DK, Finney GL, Rynes E, Maccoss M, Ramirez JA, Park H, Iritani BM PloS one 2013;8(2):e54902 PubMed | DOI

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 Bereman MS, Hsieh EJ, Corso TN, Van Pelt CK, Maccoss MJ Molecular & cellular proteomics : MCP 2013 Jun;12(6):1701-8 PubMed | DOI

Effects of column and gradient lengths on peak capacity and peptide identification in nanoflow LC-MS/MS of complex proteomic samples Hsieh EJ, Bereman MS, Durand S, Valaskovic GA, MacCoss MJ Journal of the American Society for Mass Spectrometry 2013 Jan;24(1):148-53 PubMed | DOI

Proteomic analysis of adducted butyrylcholinesterase for biomonitoring organophosphorus exposures Marsillach J, Hsieh EJ, Richter RJ, MacCoss MJ, Furlong CE Chemico-biological interactions 2013 Mar;203(1):85-90 PubMed | DOI

2012

Estimating relative abundances of proteins from shotgun proteomics data McIlwain S, Mathews M, Bereman MS, Rubel EW, MacCoss MJ, Noble WS BMC bioinformatics 2012 Nov;13:308 PubMed | DOI

Discovery and targeted LC-MS/MS of purified polerovirus reveals differences in the virus-host interactome associated with altered aphid transmission Cilia M, Peter KA, Bereman MS, Howe K, Fish T, Smith D, Gildow F, MacCoss MJ, Thannhauser TW, Gray SM PloS one 2012;7(10):e48177 PubMed | DOI

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 Nature biotechnology 2012 Oct;30(10):918-20 PubMed | DOI

De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics Egertson JD, Eng JK, Bereman MS, Hsieh EJ, Merrihew GE, MacCoss MJ Journal of the American Society for Mass Spectrometry 2012 Dec;23(12):2075-82 PubMed | DOI

An expansive human regulatory lexicon encoded in transcription factor footprints 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, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA Nature 2012 Sep;489(7414):83-90 PubMed | DOI

Learning score function parameters for improved spectrum identification in tandem mass spectrometry experiments Spivak M, Bereman MS, Maccoss MJ, Noble WS Journal of proteome research 2012 Sep;11(9):4499-508 PubMed | DOI

Topograph, a software platform for precursor enrichment corrected global protein turnover measurements Hsieh EJ, Shulman NJ, Dai DF, Vincow ES, Karunadharma PP, Pallanck L, Rabinovitch PS, MacCoss MJ Molecular & cellular proteomics : MCP 2012 Nov;11(11):1468-74 PubMed | DOI

A mass spectrometry proteomics data management platform Sharma V, Eng JK, Maccoss MJ, Riffle M Molecular & cellular proteomics : MCP 2012 Sep;11(9):824-31 PubMed | DOI

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 PubMed | DOI

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 PubMed | DOI

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 Journal of proteome research 2012 Jun;11(6):3467-79 PubMed | DOI

A method to determine the kinetics of multiple proteins in human infants with respiratory distress syndrome Bereman MS, Tomazela DM, Heins HS, Simonato M, Cogo PE, Hamvas A, Patterson BW, Cole FS, MacCoss MJ Analytical and bioanalytical chemistry 2012 Jun;403(8):2397-402 PubMed | DOI

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 Molecular & cellular proteomics : MCP 2012 May;11(5):202-14 PubMed | DOI

Identification of peptide features in precursor spectra using Hardklör and Krönik Hoopmann MR, MacCoss MJ, Moritz RL Current protocols in bioinformatics 2012 Mar;Chapter 13:Unit13.18 PubMed | DOI

Computational and statistical analysis of protein mass spectrometry data Noble WS, MacCoss MJ PLoS computational biology 2012 Jan;8(1):e1002296 PubMed | DOI

Capillary electrophoresis with Orbitrap-Velos mass spectrometry detection Wojcik R, Li Y, Maccoss MJ, Dovichi NJ Talanta 2012 Jan;88:324-9 PubMed | DOI

Evaluation of front-end higher energy collision-induced dissociation on a benchtop dual-pressure linear ion trap mass spectrometer for shotgun proteomics Bereman MS, Canterbury JD, Egertson JD, Horner J, Remes PM, Schwartz J, Zabrouskov V, MacCoss MJ Analytical chemistry 2012 Feb;84(3):1533-9 PubMed | DOI

Direct maximization of protein identifications from tandem mass spectra Spivak M, Weston J, Tomazela D, MacCoss MJ, Noble WS Molecular & cellular proteomics : MCP 2012 Feb;11(2):M111.012161 PubMed | DOI

Mitochondrial proteome remodelling in pressure overload-induced heart failure: the role of mitochondrial oxidative stress Dai DF, Hsieh EJ, Liu Y, Chen T, Beyer RP, Chin MT, MacCoss MJ, Rabinovitch PS Cardiovascular research 2012 Jan;93(1):79-88 PubMed | DOI

2011

Rapid empirical discovery of optimal peptides for targeted proteomics Stergachis AB, MacLean B, Lee K, Stamatoyannopoulos JA, MacCoss MJ Nature methods 2011 Nov;8(12):1041-3 PubMed | DOI

Garrod’s fourth inborn error of metabolism solved by the identification of mutations causing pentosuria 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 Proceedings of the National Academy of Sciences of the United States of America 2011 Nov;108(45):18313-7 PubMed | DOI

Biomarkers of organophosphorus (OP) exposures in humans Marsillach J, Richter RJ, Kim JH, Stevens RC, MacCoss MJ, Tomazela D, Suzuki SM, Schopfer LM, Lockridge O, Furlong CE Neurotoxicology 2011 Oct;32(5):656-60 PubMed | DOI

Comparative proteomics reveals deficiency of SLC9A1 (sodium/hydrogen exchanger NHE1) in β-adducin null red cells Wooden JM, Finney GL, Rynes E, Maccoss MJ, Lambert AJ, Robledo RF, Peters LL, Gilligan DM British journal of haematology 2011 Aug;154(4):492-501 PubMed | DOI

Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling Dean MD, Findlay GD, Hoopmann MR, Wu CC, MacCoss MJ, Swanson WJ, Nachman MW BMC genomics 2011 Jun;12:306 PubMed | DOI

Comparison between procedures using SDS for shotgun proteomic analyses of complex samples Bereman MS, Egertson JD, MacCoss MJ Proteomics 2011 Jul;11(14):2931-5 PubMed | DOI

Comparative proteomics reveals deficiency of NHE-1 (Slc9a1) in RBCs from the beta-adducin knockout mouse model of hemolytic anemia Gilligan DM, Finney GL, Rynes E, Maccoss MJ, Lambert AJ, Peters LL, Robledo RF, Wooden JM Blood cells, molecules & diseases 2011 Aug;47(2):85-94 PubMed | DOI

ABRF-PRG07: advanced quantitative proteomics study Falick AM, Lane WS, Lilley KS, MacCoss MJ, Phinney BS, Sherman NE, Weintraub ST, Witkowska HE, Yates NA Journal of biomolecular techniques : JBT 2011 Apr;22(1):21-6 PubMed

The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses 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, Turck CW Proteomics 2011 Apr;11(8):1371-81 PubMed | DOI

2010

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project 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, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH Science (New York, N.Y.) 2010 Dec;330(6012):1775-87 PubMed | DOI

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 Analytical chemistry 2010 Dec;82(24):10116-24 PubMed | DOI

An E3 ubiquitin ligase prevents ectopic localization of the centromeric histone H3 variant via the centromere targeting domain Ranjitkar P, Press MO, Yi X, Baker R, MacCoss MJ, Biggins S Molecular cell 2010 Nov;40(3):455-64 PubMed | DOI

Precursor charge state prediction for electron transfer dissociation tandem mass spectra Sharma V, Eng JK, Feldman S, von Haller PD, MacCoss MJ, Noble WS Journal of proteome research 2010 Oct;9(10):5438-44 PubMed | DOI

Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data Serang O, MacCoss MJ, Noble WS Journal of proteome research 2010 Oct;9(10):5346-57 PubMed | DOI

Functional diversification and evolution of antifreeze proteins in the antarctic fish Lycodichthys dearborni Kelley JL, Aagaard JE, MacCoss MJ, Swanson WJ Journal of molecular evolution 2010 Aug;71(2):111-8 PubMed | DOI

Nitric-oxide synthase forms N-NO-pterin and S-NO-cys: implications for activity, allostery, and regulation Rosenfeld RJ, Bonaventura J, Szymczyna BR, MacCoss MJ, Arvai AS, Yates JR, Tainer JA, Getzoff ED The Journal of biological chemistry 2010 Oct;285(41):31581-9 PubMed | DOI

Mitochondrial dysfunction in NnaD mutant flies and Purkinje cell degeneration mice reveals a role for Nna proteins in neuronal bioenergetics 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, Hook V, Bennett CL, Pallanck LJ, La Spada AR Neuron 2010 Jun;66(6):835-47 PubMed | DOI

High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection Cooper SJ, Finney GL, Brown SL, Nelson SK, Hesselberth J, MacCoss MJ, Fields S Genome research 2010 Sep;20(9):1288-96 PubMed | DOI

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 Zelter A, Hoopmann MR, Vernon R, Baker D, MacCoss MJ, Davis TN Journal of proteome research 2010 Jul;9(7):3583-9 PubMed | DOI

A high voltage asymmetric waveform generator for FAIMS Canterbury JD, Gladden J, Buck L, Olund R, MacCoss MJ Journal of the American Society for Mass Spectrometry 2010 Jul;21(7):1118-21 PubMed | DOI

Identification and characterization of biomarkers of organophosphorus exposures in humans Kim JH, Stevens RC, MacCoss MJ, Goodlett DR, Scherl A, Richter RJ, Suzuki SM, Furlong CE Advances in experimental medicine and biology 2010;660:61-71 PubMed | DOI

Measurement of human surfactant protein-B turnover in vivo from tracheal aspirates using targeted proteomics Tomazela DM, Patterson BW, Hanson E, Spence KL, Kanion TB, Salinger DH, Vicini P, Barret H, Heins HB, Cole FS, Hamvas A, MacCoss MJ Analytical chemistry 2010 Mar;82(6):2561-7 PubMed | DOI

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 (Oxford, England) 2010 Apr;26(7):966-8 PubMed | DOI

Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry Bern M, Finney G, Hoopmann MR, Merrihew G, Toth MJ, MacCoss MJ Analytical chemistry 2010 Feb;82(3):833-41 PubMed | DOI

Comparison of database search strategies for high precursor mass accuracy MS/MS data Hsieh EJ, Hoopmann MR, MacLean B, MacCoss MJ Journal of proteome research 2010 Feb;9(2):1138-43 PubMed | DOI

ZP domain proteins in the abalone egg coat include a paralog of VERL under positive selection that binds lysin and 18-kDa sperm proteins Aagaard JE, Vacquier VD, MacCoss MJ, Swanson WJ Molecular biology and evolution 2010 Jan;27(1):193-203 PubMed | DOI

2009

Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures Second TP, Blethrow JD, Schwartz JC, Merrihew GE, MacCoss MJ, Swaney DL, Russell JD, Coon JJ, Zabrouskov V Analytical chemistry 2009 Sep;81(18):7757-65 PubMed | DOI

Bindin from a sea star Patiño S, Aagaard JE, MacCoss MJ, Swanson WJ, Hart MW Evolution & development 2009;11(4):376-81 PubMed | DOI

Bruton’s tyrosine kinase revealed as a negative regulator of Wnt-beta-catenin signaling James RG, Biechele TL, Conrad WH, Camp ND, Fass DM, Major MB, Sommer K, Yi X, Roberts BS, Cleary MA, Arthur WT, MacCoss M, Rawlings DJ, Haggarty SJ, Moon RT Science signaling 2009 May;2(72):ra25 PubMed | DOI

Overexpression of catalase targeted to mitochondria attenuates murine cardiac aging Dai DF, Santana LF, Vermulst M, Tomazela DM, Emond MJ, MacCoss MJ, Gollahon K, Martin GM, Loeb LA, Ladiges WC, Rabinovitch PS Circulation 2009 Jun;119(21):2789-97 PubMed | DOI

Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus) Dean MD, Clark NL, Findlay GD, Karn RC, Yi X, Swanson WJ, MacCoss MJ, Nachman MW Molecular biology and evolution 2009 Aug;26(8):1733-43 PubMed | DOI

Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila Findlay GD, MacCoss MJ, Swanson WJ Genome research 2009 May;19(5):886-96 PubMed | DOI

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 Journal of proteome research 2009 Jun;8(6):2733-9 PubMed | DOI

Post analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures Hoopmann MR, Merrihew GE, von Haller PD, MacCoss MJ Journal of proteome research 2009 Apr;8(4):1870-5 PubMed | DOI

2008

New regulators of Wnt/beta-catenin signaling revealed by integrative molecular screening Major MB, Roberts BS, Berndt JD, Marine S, Anastas J, Chung N, Ferrer M, Yi X, Stoick-Cooper CL, von Haller PD, Kategaya L, Chien A, Angers S, MacCoss M, Cleary MA, Arthur WT, Moon RT Science signaling 2008 Nov;1(45):ra12 PubMed | DOI

High quality catalog of proteotypic peptides from human heart Kline KG, Frewen B, Bristow MR, Maccoss MJ, Wu CC Journal of proteome research 2008 Nov;7(11):5055-61 PubMed | DOI

A fast SEQUEST cross correlation algorithm Eng JK, Fischer B, Grossmann J, Maccoss MJ Journal of proteome research 2008 Oct;7(10):4598-602 PubMed | DOI

Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics Canterbury JD, Yi X, Hoopmann MR, MacCoss MJ Analytical chemistry 2008 Sep;80(18):6888-97 PubMed | DOI

Proteomics reveals novel Drosophila seminal fluid proteins transferred at mating Findlay GD, Yi X, Maccoss MJ, Swanson WJ PLoS biology 2008 Jul;6(7):e178 PubMed | DOI

Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations Merrihew GE, Davis C, Ewing B, Williams G, Käll L, Frewen BE, Noble WS, Green P, Thomas JH, MacCoss MJ Genome research 2008 Oct;18(10):1660-9 PubMed | DOI

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification Klammer AA, Reynolds SM, Bilmes JA, MacCoss MJ, Noble WS Bioinformatics (Oxford, England) 2008 Jul;24(13):i348-56 PubMed | DOI

Rapid and accurate peptide identification from tandem mass spectra Park CY, Klammer AA, Käll L, MacCoss MJ, Noble WS Journal of proteome research 2008 Jul;7(7):3022-7 PubMed | DOI

Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data Finney GL, Blackler AR, Hoopmann MR, Canterbury JD, Wu CC, MacCoss MJ Analytical chemistry 2008 Feb;80(4):961-71 PubMed | DOI

Proteomic solutions for analytical challenges associated with alcohol research MacCoss MJ, Wu CC Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism 2008;31(3):251-5 PubMed

Assigning significance to peptides identified by tandem mass spectrometry using decoy databases Käll L, Storey JD, MacCoss MJ, Noble WS Journal of proteome research 2008 Jan;7(1):29-34 PubMed | DOI

Posterior error probabilities and false discovery rates: two sides of the same coin Käll L, Storey JD, MacCoss MJ, Noble WS Journal of proteome research 2008 Jan;7(1):40-4 PubMed | DOI

2007

Using BiblioSpec for creating and searching tandem MS peptide libraries Frewen B, MacCoss MJ Current protocols in bioinformatics 2007 Dec;Chapter 13:13.7.1-13.7.12 PubMed | DOI

Semi-supervised learning for peptide identification from shotgun proteomics datasets Käll L, Canterbury JD, Weston J, Noble WS, MacCoss MJ Nature methods 2007 Nov;4(11):923-5 PubMed | DOI

Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway Mayor T, Graumann J, Bryan J, MacCoss MJ, Deshaies RJ Molecular & cellular proteomics : MCP 2007 Nov;6(11):1885-95 PubMed | DOI

Duplication and selection on abalone sperm lysin in an allopatric population Clark NL, Findlay GD, Yi X, MacCoss MJ, Swanson WJ Molecular biology and evolution 2007 Sep;24(9):2081-90 PubMed | DOI

Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions Klammer AA, Yi X, MacCoss MJ, Noble WS Analytical chemistry 2007 Aug;79(16):6111-8 PubMed | DOI

High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry Hoopmann MR, Finney GL, MacCoss MJ Analytical chemistry 2007 Aug;79(15):5620-32 PubMed | DOI

Wilms tumor suppressor WTX negatively regulates WNT/beta-catenin signaling Major MB, Camp ND, Berndt JD, Yi X, Goldenberg SJ, Hubbert C, Biechele TL, Gingras AC, Zheng N, Maccoss MJ, Angers S, Moon RT Science (New York, N.Y.) 2007 May;316(5827):1043-6 PubMed | DOI

Quantitative proteomic analysis of mammalian organisms using metabolically labeled tissues Wu CC, MacCoss MJ Methods in molecular biology (Clifton, N.J.) 2007;359:191-201 PubMed | DOI

Computational analysis of quantitative proteomics data using stable isotope labeling MacCoss MJ, Wu CC Methods in molecular biology (Clifton, N.J.) 2007;359:177-89 PubMed | DOI

Estrogen receptor alpha is a putative substrate for the BRCA1 ubiquitin ligase Eakin CM, Maccoss MJ, Finney GL, Klevit RE Proceedings of the National Academy of Sciences of the United States of America 2007 Apr;104(14):5794-9 PubMed | DOI

A major deletion in the surfactant protein-B gene causing lethal respiratory distress Wegner DJ, Hertzberg T, Heins HB, Elmberger G, MacCoss MJ, Carlson CS, Nogee LM, Cole FS, Hamvas A Acta paediatrica (Oslo, Norway : 1992) 2007 Apr;96(4):516-20 PubMed | DOI

2006

Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs Aagaard JE, Yi X, MacCoss MJ, Swanson WJ Proceedings of the National Academy of Sciences of the United States of America 2006 Nov;103(46):17302-7 PubMed | DOI

Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery Angers S, Li T, Yi X, MacCoss MJ, Moon RT, Zheng N Nature 2006 Oct;443(7111):590-3 PubMed | DOI

Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries Frewen BE, Merrihew GE, Wu CC, Noble WS, MacCoss MJ Analytical chemistry 2006 Aug;78(16):5678-84 PubMed | DOI

The KLHL12-Cullin-3 ubiquitin ligase negatively regulates the Wnt-beta-catenin pathway by targeting Dishevelled for degradation Angers S, Thorpe CJ, Biechele TL, Goldenberg SJ, Zheng N, MacCoss MJ, Moon RT Nature cell biology 2006 Apr;8(4):348-57 PubMed | DOI

Effects of modified digestion schemes on the identification of proteins from complex mixtures Klammer AA, MacCoss MJ Journal of proteome research 2006 Mar;5(3):695-700 PubMed | DOI

Quantitative comparison of proteomic data quality between a 2D and 3D quadrupole ion trap Blackler AR, Klammer AA, MacCoss MJ, Wu CC Analytical chemistry 2006 Feb;78(4):1337-44 PubMed | DOI

2005

Peptide charge state determination for low-resolution tandem mass spectra Klammer AA, Wu CC, MacCoss MJ, Noble WS Proceedings. IEEE Computational Systems Bioinformatics Conference 2005:175-85 PubMed | DOI

Measurement of the isotope enrichment of stable isotope-labeled proteins using high-resolution mass spectra of peptides MacCoss MJ, Wu CC, Matthews DE, Yates JR Analytical chemistry 2005 Dec;77(23):7646-53 PubMed | DOI

Quantitative MS for proteomics: teaching a new dog old tricks MacCoss MJ, Matthews DE Analytical chemistry 2005 Aug;77(15):294A-302A PubMed | DOI

Aminoglycoside antibiotics induce bacterial biofilm formation Hoffman LR, D’Argenio DA, MacCoss MJ, Zhang Z, Jones RA, Miller SI Nature 2005 Aug;436(7054):1171-5 PubMed | DOI

A glutamate-alanine-leucine (EAL) domain protein of Salmonella controls bacterial survival in mice, antioxidant defence and killing of macrophages: role of cyclic diGMP Hisert KB, MacCoss M, Shiloh MU, Darwin KH, Singh S, Jones RA, Ehrt S, Zhang Z, Gaffney BL, Gandotra S, Holden DW, Murray D, Nathan C Molecular microbiology 2005 Jun;56(5):1234-45 PubMed | DOI

Computational analysis of shotgun proteomics data MacCoss MJ Current opinion in chemical biology 2005 Feb;9(1):88-94 PubMed | DOI

2004

Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis Wu CC, MacCoss MJ, Howell KE, Matthews DE, Yates JR Analytical chemistry 2004 Sep;76(17):4951-9 PubMed | DOI

MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications McDonald WH, Tabb DL, Sadygov RG, MacCoss MJ, Venable J, Graumann J, Johnson JR, Cociorva D, Yates JR Rapid communications in mass spectrometry : RCM 2004;18(18):2162-8 PubMed | DOI

Evidence for a post-translational modification, aspartyl aldehyde, in a photosynthetic membrane protein Anderson LB, Ouellette AJ, Eaton-Rye J, Maderia M, MacCoss MJ, Yates JR, Barry BA Journal of the American Chemical Society 2004 Jul;126(27):8399-405 PubMed | DOI

Organellar proteomics reveals Golgi arginine dimethylation Wu CC, MacCoss MJ, Mardones G, Finnigan C, Mogelsvang S, Yates JR, Howell KE Molecular biology of the cell 2004 Jun;15(6):2907-19 PubMed | DOI

2003

A correlation algorithm for the automated quantitative analysis of shotgun proteomics data MacCoss MJ, Wu CC, Liu H, Sadygov R, Yates JR Analytical chemistry 2003 Dec;75(24):6912-21 PubMed | DOI

Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility Tabb DL, MacCoss MJ, Wu CC, Anderson SD, Yates JR Analytical chemistry 2003 May;75(10):2470-7 PubMed | DOI

A method for the comprehensive proteomic analysis of membrane proteins Wu CC, MacCoss MJ, Howell KE, Yates JR Nature biotechnology 2003 May;21(5):532-8 PubMed | DOI

2002

Code developments to improve the efficiency of automated MS/MS spectra interpretation Sadygov RG, Eng J, Durr E, Saraf A, McDonald H, MacCoss MJ, Yates JR Journal of proteome research 2002;1(3):211-5 PubMed | DOI

Probability-based validation of protein identifications using a modified SEQUEST algorithm MacCoss MJ, Wu CC, Yates JR Analytical chemistry 2002 Nov;74(21):5593-9 PubMed | DOI

Posttranslational modifications in the CP43 subunit of photosystem II Anderson LB, Maderia M, Ouellette AJ, Putnam-Evans C, Higgins L, Krick T, MacCoss MJ, Lim H, Yates JR, Barry BA Proceedings of the National Academy of Sciences of the United States of America 2002 Nov;99(23):14676-81 PubMed | DOI

Shotgun proteomics: tools for the analysis of complex biological systems Wu CC, MacCoss MJ Current opinion in molecular therapeutics 2002 Jun;4(3):242-50 PubMed

Shotgun identification of protein modifications from protein complexes and lens tissue MacCoss MJ, McDonald WH, Saraf A, Sadygov R, Clark JM, Tasto JJ, Gould KL, Wolters D, Washburn M, Weiss A, Clark JI, Yates JR Proceedings of the National Academy of Sciences of the United States of America 2002 Jun;99(12):7900-5 PubMed | DOI

2001

Proteomics: analytical tools and techniques MacCoss MJ, Yates JR Current opinion in clinical nutrition and metabolic care 2001 Sep;4(5):369-75 PubMed | DOI

Evaluation and optimization of ion-current ratio measurements by selected-ion-monitoring mass spectrometry MacCoss MJ, Toth MJ, Matthews DE Analytical chemistry 2001 Jul;73(13):2976-84 PubMed | DOI

Recovery of (13)CO(2) from infused [1-(13)C]leucine and [1,2-(13)C(2)]leucine in healthy humans Toth MJ, MacCoss MJ, Poehlman ET, Matthews DE American journal of physiology. Endocrinology and metabolism 2001 Aug;281(2):E233-41 PubMed | DOI

Measurement of intracellular sulfur amino acid metabolism in humans MacCoss MJ, Fukagawa NK, Matthews DE American journal of physiology. Endocrinology and metabolism 2001 Jun;280(6):E947-55 PubMed | DOI

Effects of estradiol and progesterone on body composition, protein synthesis, and lipoprotein lipase in rats Toth MJ, Poehlman ET, Matthews DE, Tchernof A, MacCoss MJ American journal of physiology. Endocrinology and metabolism 2001 Mar;280(3):E496-501 PubMed | DOI

1999

Measurement of homocysteine concentrations and stable isotope tracer enrichments in human plasma MacCoss MJ, Fukagawa NK, Matthews DE Analytical chemistry 1999 Oct;71(20):4527-33 PubMed | DOI

1995

Direct database searching with MALDI-PSD spectra of peptides Griffin PR, MacCoss MJ, Eng JK, Blevins RA, Aaronson JS, Yates JR Rapid communications in mass spectrometry : RCM 1995;9(15):1546-51 PubMed | DOI