Our Journal Cover Articles

 
 

Original Research Articles & Protocols

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+ 2024

  1. Wojtkiewicz M, Subramanian SP, Gundry RL, Multinozzle emitter for improved negative mode analysis of reduced native N-glycans by microflow porous graphitized carbon liquid chromatography mass spectrometry. Analytical Chemistry, PMID:38556995.**Selected for Supplementary Journal Cover


  2. Berg Luecke L, Mesidor R, Littrell J, Carpenter M, Wojtkiewicz M, Gundry RL. Veneer Is a Webtool for Rapid, Standardized, and Transparent Interpretation, Annotation, and Reporting of Mammalian Cell Surface N-Glycocapture Data. Journal of Proteome Research, PMID:38412263. **Selected for Supplementary Journal Cover


  3. Waknitz M, Berg Luecke L, Mesidor R, Wojtkiewicz M, Castro C, Gundry RL.The GENTIL Method for Isolation of Human Adult Cardiomyocytes from Cryopreserved Tissue for Proteomic Analyses. Methods in Molecular Biology, PMID:38038848.

+ 2023

  1. Yeo CT, Kropp EM, Hansen PA, Pereckas M, Oleson BJ, Naatz A, Stancill JS, Ross KA, Gundry RL, Corbett JA. β-cell selective inhibition of DNA damage response signaling by nitric oxide is associated with an attenuation in glucose uptake. Journal of Biological Chemistry, PMID: 36773802.

  1. Berg Luecke L, Waas M, Littrell J, Wojtkiewicz M, Castro C, Burkovetskaya M, Schuette EN, Buchberger AR, Churko J, Chalise C, Waknitz M, Konfrst S, Teuben R, Morrissette-McAlmon J, Mahr C, Anderson DR, Boheler KR, Gundry RL, Surfaceome mapping of primary human heart cells with CellSurfer uncovers novel cardiomyocyte surface protein LSMEM2 and proteome dynamics in failing hearts. Nature Cardiovascular Research, 2, 76–95. PMID:36950336.

+ 2022

  1. Farnoodian M, Bose D, Khristov V, Susaimanickam PJ, Maddileti S, Mariappan I, Abu-Asab M, Campos M, Villasmil R, Wan Q, Maminishkis A, McGaughey D, Barone F, Gundry RL, Riordon DR, Boheler KR, Sharma R, Bharti K. Cell-Autonomous lipid-handling defects in Stargardt iPSC-derived retinal pigment epithelium cells. Stem Cell Reports, 17(11):2438-2450 PMID: 36306781.
  2. Medcalf MR, Bantis LE, Shi P, Bhadbhade P, Gundry RL, Mikuls TR, England BR, O'Dell JR, Funk RS., Plasma metabolic profiling as a tool to identify predictive biomarkers of methotrexate efficacy in rheumatoid arthritis. Semin Arthritis Rheum., 56:152056. PMID: 34940582.

+ 2021

  1. Medcalf MR, Bhadbhade P, Mikuls T, O’Dell JR, Gundry RL, Funk RS, Plasma Metabolome Normalization in Rheumatoid Arthritis Following Initiation of Methotrexate and the Identification of Metabolic Biomarkers of Efficacy, Metabolites, 11(12): 824. PMID: 34940582.**Selected for Journal Cover

  2. Jiang X, Wojtkiewicz M, Patwardhan C, Greer S, Kong Y, Kuss M, Huang X, Liao J, Lu Y, Dudley A, Gundry RL, Fuchs M, Streubel P, Duan B, The effects of maturation and aging on the rotator cuff tendon-to-bone interface, FASEB J, Dec;35(12):e22066. PMID: 34822203.

  3. Wojtkiewicz M, Berg Luecke L, Castro C, Burkovetskaya M, Mesidor R, Gundry RL, Bottom-up proteomic analysis of human adult cardiac tissue and isolated cardiomyocytes, Journal of Molecular and Cellular Cardiology, 162:20-31. PMID: 34437879.

  4. Whyte ML, Smith K, Buchberger A, Berg Luecke L, Tjan LH, Mori L, Gundry RL, Hudson AW, The Roseoloviruses Downregulate the Protein Tyrosine Phosphatase PTPRC (CD45), Journal of Virology, 2021,95(14):e0162820. PMID: 33952641.

  5. Wojtkiewicz M, Berg Luecke L, Kelly MI, Gundry RL, Facile Preparation of Peptides for Mass Spectrometry Analysis in Bottom-Up Proteomics Workflows, Current Protocols in Molecular Biology, 2021, 1(3):e85. PMID: 33750040.

  6. Berg Luecke L, Gundry RL, Assessment of Streptavidin Bead Binding Capacity to Improve Quality of Streptavidin-based Enrichment Studies, Journal of Proteome Research, 2021, 20(2):1153-1164. PMID: 33270449. **Selected for Supplementary Journal Cover

  7. Fehrenbach D, Abais-Battad J, Dasinger J, Lund H, Keppel T, Zemaj J, Gundry RL, Geurts A, Dwinell M, Mattson D, Sexual Dimorphic Role of CD14 in Salt Sensitive Hypertension and Renal Injury. Hypertension, 77(1):228-240, 2021. PMID: 33249861 **Selected for Invited Editorial Commentary

+ 2020

  1. Oldham RAA, Faber ML, Keppel TR, Buchberger AR, Waas M, Hari P, Gundry RL, Medin JA, Discovery and validation of surface N-glycoproteins in MM cell lines and patient samples uncovers immunotherapy targets, Journal for ImmunoTherapy of Cancer, e000915. doi: 10.1136/jitc-2020-000915, 2020. PMID: 32771993.

  2. Waas M, Littrell J, Gundry RL, CIRFESS: An interactive resource for querying the set of theoretically detectable peptides for cell surface and extracellular enrichment proteomic studies, Journal of the American Society for Mass Spectrometry, 2020, 31(7):1389-1397. PMID: 32212654.**Selected for Journal Cover

  3. Kanack AJ, Vittal A, Keppel T, Gundry RL, Klevit RE, Scaglione KM, UbcH5 interacts with substrates to facilitate lysine selection with the E3 ubiquitin ligase CHIP. Biochemistry, 59(22):2078-2088, 2020. PMID: 32401531.

  4. Waas M, Snarrenberg ST, Littrell J, Jones Lipinski RA, Hansen P, Corbett J, Gundry RL, SurfaceGenie: A web-based application for integrating predictive and experimental data for rational candidate surface marker prioritization, Bioinformatics, 36(11), 3447–3456, 2020. PMID: 32053146.

  5. Wu PK, Hong SK, Gundry RL, Lin CW, Shao H, Gestwicki J, Park JI, Mortalin/HSPA9 targeting selectively induces B-RafV600E tumor cell lethality by perturbing mitochondrial membrane permeability via adenine nucleotide translocase 3. Science Signaling, 13(622):eaay1478, 2020. PMID: 32156782. **Selected for Journal Highlight

  6. Young J; Keppel T; Waas M; Salmon A; Buchberger A; Skumatz C; Gundry RL**#; Kassem I#**, Quantitative proteomic analysis of aqueous humor after rabbit lensectomy reveals differences in coagulation and immunomodulatory proteins. Molecular Omics, 16(2):126-137, 2020. PMID: 32031200. #Co-corresponding authors **Selected for Journal Cover

  7. Poon EN, Luo X, Yan B, Wu S, Yong Y, Shao J, Webb SE, Gundry RL, Yang HT, Boheler KR, CD36 identifies a sub-population of mitochondria-rich cardiomyocytes that reduces interline variability among hPSCs. Cell Research, 30(7):626-629,2020. PMID: 32157205.

  8. Ashwood C, Waas M, Weerasekera R, Gundry RL, Reference glycan structure libraries of primary human cardiomyocytes and pluripotent stem cell-derived cardiomyocytes reveal cell-type and culture stage-specific glycan phenotypes, Journal of Molecular and Cellular Cardiology, 139:33-46, 2020. PMID 31972267. **Selected for Journal Cover

+ 2019

  1. Ashwood C, Pratt B, MacLean B, Gundry RLL, Packer NH, Standardization of PGC-LC-MS-based glycomics for sample specific glycotyping, Analyst, 144(11):3601-3612, 2019. PMID: 31065629.

  2. Berg Luecke L, Waas M, Gundry RL Reliable Protocols for Flow Cytometry Analysis of Intracellular Proteins in Pluripotent Stem Cell Derivatives: A Fit-For-Purpose Approach. Current Protocols in Stem Cell Biology, 2019 Sep;50(1):e94, 2019. PMID:31479597.

  1. Waas M, Pereckas M, Jones Lipinski R, Ashwood, C, Gundry RL, SP2: Rapid and Automatible Contaminant Removal from Peptide Samples for Proteomic Analyses, Journal of Proteome Research, 18(4):1644-1656, 2019. PMID 30795648.

  2. Waas M, Weerasekera R, Kropp EM, Romero M, Poon E, Boheler KR, Burridge PW, Gundry RL, Are these cardiomyocytes? Protocol development reveals impact of sample preparation on the accuracy of identifying cardiomyocytes by flow cytometry. Stem Cell Reports, 12(2):395-410, 2019, PMID: 30686762.

+ 2018

  1. Moehring F, Waas M, Keppel TR, Rathore D, Reynolds A, Stucky CL**#, Gundry RL#**, Quantitative top down mass spectrometry identifies proteoforms differentially secreted by mechanical stimulation of mouse skin. Journal of Proteome Research, 17(8): 2635-2648, 2018. PMID: 29925238. **#**Co-corresponding authors.

  2. Fujinaka CM, Waas M, Gundry RL, Mass Spectrometry Based Identification of Extracellular Domains of Cell Surface N-Glycoproteins: Defining the Accessible Surfaceome for Immunophenotyping Stem Cells and their Derivatives in Methods in Molecular Biology: The Surfaceome, Eds Boheler KR and Gundry RL, Humana Press, Volume 1722, 2018. PMID: 29264798.


+ 2017

  1. Haverland NA#, Waas M#, Ntai I, Keppel T, Gundry RL, Kelleher NK, Cell Surface Proteomics of N-Linked Glycoproteins for Typing of Human Lymphocytes. Proteomics, 17(19), 2017. PMID: 28834292. #Denotes equal contribution. **Selected for Journal Cover

  2. Kropp EM, Broniowska KA, Waas M, Corbett JA, Gundry RL, Cardiomyocyte differentiation promotes cell survival during NAMPT inhibition through increased maintenance of cellular energy stores. Stem Cells Translational Medicine, 6; 1191-1201, 2017. PMID: 28224719. **Selected for Journal Cover

  3. Mallanna SK, Waas M, Duncan SA, Gundry RL, N-Glycoprotein Surfaceome of Human Induced Pluripotent Stem Cell Derived Hepatic Endoderm, Proteomics, 7(5), 2017. PMID: 27966262.

+ 2016

  1. Mallanna SK, Cayo MA, Twaroski K, Gundry RL, Duncan SA, Mapping the Cell Surface N-Glycoproteome of Human Hepatocytes Reveals New Markers for Selecting Homogeneous Populations of Pluripotent Stem Cell-Derived Hepatocyte-Like Cells, Stem Cell Reports, 7(3): 543-56, 2016. PMID: 27569060.

+ 2015

  1. Bausch-Fluck D, Hofmann A, Bock T, Frei AP, Cerciello F, Jacobs A, Moest H, Omasits U, Gundry RL, Yoon C, Schiess R, Schmidt A, Mirkowska P, Härtlová A, Van Eyk JE, Bourquin JP; Aebersold R, Boheler KR, Zandstra P, Wollscheid B, A Mass Spectrometric-Derived Cell Surface Protein Atlas, PLoS One, 10(3): e021314, 2015. PMID: 25894527.

  2. Olson LJ, Jensen DR, Volkman BF, Kim JJP, Peterson FC, Gundry RL, Dahms N. Bacterial expression of the phosphodiester-binding site of the cation-independent mannose 6-phosphate receptor for crystallographic and NMR studies, Protein Expression and Purification, 111, 91-97, 2015. PMID: 25863146.

  3. Kropp EM, Oleson B, Bhattacharya S, Chuppa SL, Chadwick AC, Sahoo D, Diers-Dranka A, Hogg N, Boheler KR, Corbett JA, Gundry RL, Inhibition of an NAD+ Salvage Pathway Provides Efficient and Selective Toxicity to Human Pluripotent Stem Cells, Stem Cells Translational Medicine, 4(5), 483-93, 2015. PMID: 25834119.

  4. Thomas MA, Buelow BJ, Nevins AM, Jones SE, Peterson FC, Gundry RL, Grayson MH, Volkman BF, Structure-function analysis of CCL28 in the development of post-viral asthma, Journal of Biological Chemistry, 290(7), 4528-36, 2015. PMID: 25556652.

  5. Kim MS, Horst A, Blinka S, Stamm K, Schuman J, Gundry RLL, Tomita-Mitchell A, Lough J, Activin-A and Bmp4 levels modulate cell type specification during CHIR-induced cardiomyogenesis, PLoS One, 10(2):e0118670, 2015. PMID: 25706534.

+ 2014

  1. Kropp EM, Bhattacharya S, Waas M, Chuppa SL, Hadjantonakis AK, Boheler KR, Gundry RL, N-Glycoprotein Surfaceomes of Four Developmentally Distinct Mouse Cell Types, Proteomics – Clinical Applications, 8(7-8), 603-609, 2014. PMID: 24920426.

  2. Boheler KR, Bhattacharya S, Chuppa S, Riordon DR, Kropp E, Burridge PW, Wu JC, Wersto RP, Rao S, Wollscheid B, Gundry RL, A Human Pluripotent Stem Cell Surface N-Glycoproteome Resource Reveals Markers, Extracellular Epitopes, and Drug Targets, Stem Cell Reports, 3(1), 185-203, 2014. PMID: 25068131.

  3. Bhattacharya S, Burridge PW, Kropp EM, Chuppa SL, Kwok WM, Wu JC, Boheler KR, Gundry RL, High Efficiency Differentiation of Human Pluripotent Stem Cells to Cardiomyocytes and Characterization by Flow Cytometry, Journal of Visualized Experiments, 91(52010), 2014. PMID: 25286293.

  4. Waas M, Bhattacharya S, Chuppa S, Wu X, Jensen DR, Omasits U, Wollscheid D, Volkman BF, Noon KR, Gundry RL Combine and Conquer: Surfactants, solvents, and chaotropes for robust membrane protein mass spectrometry analysis, Analytical Chemistry, 86(3), 1551-9, 2014. PMID: 24392666.

+ Pre-2013

  1. Gundry RL# §, Riordon DR, Tarasova Y, Chuppa S, Bhattacharya S, Juhasz O, Wiedemeier O,  Milanovich S, Noto FK, Tchernyshyov I, Raginski K, Bausch-Fluck D,  Tae H, Marshall S, Duncan SA, Wollscheid B, Wersto RP, Rao S, Van Eyk JE, Boheler KR#, " A Cell Surfaceome Map for Immunophenotyping and Sorting Pluripotent Stem Cells", Molecular and Cellular Proteomics, 11(8):303-16, 2012. PMID: 22493178**. **#Co-corresponding authors.

  2. Boheler KR, Joodi RJ, Qiao H, Juhasz O, Urick AU, Chuppa  S, Gundry RL Wersto RP, Zhou R "Embryonic Stem Cell-derived Cardiomyocyte Heterogeneity and the Isolation of Immature and Committed Cells for Cardiac Remodeling and Regeneration", Stem Cells International, 2011:214203, 2011. PMID: 21912557.

  3. Gundry RL, Tchernyshyov I, Sheng S, Tarasova Y, Raginski K,  Boheler KR, Van Eyk JE, Expanding the mouse embryonic stem cell proteome: combining three proteomic approaches, Proteomics, 10 (14), 2728–2732, 2010. PMID: 20512790.

  4. Gundry RL, Raginski K, Tarasova Y, Tchernyshyov I,  Bausch-Fluck D, Elliott ST, Boheler KR, Van Eyk JE, Wollscheid B, The Mouse C2C12 Myoblast Cell Surface N-Linked Glycoproteome: Identification, Glycosite Occupancy, and Membrane Orientation, Molecular and Cellular Proteomics, 8(11), 2555–2569, 2009. PMID: 19656770.

  5. Gundry RL, White MY, Tchernyshyov I, Nogee J, Van Eyk, JE, Assessment of albumin removal from an immunoaffinity spin column: critical implications for proteomic examination of the albuminome and albumin-depleted samples, Proteomics, 9(7), 2021-2028, 2009. PMID: 19294703.

  6. Gundry RL#, White MY, Murray C, Kane L, Fu Q, Stanley B, Van Eyk JE, Preparation of Proteins and Peptides for Mass Spectrometry Analysis in a Bottom-Up Proteomics Workflow, Curent Protocols in Molecular Biology. Chapter 10:Unit10.25, 2009. PMID: 19816929. #Corresponding author.

  7. Li W, Malpica T, Gundry RL, Cotter RJ, McArthur J, Sacktor, N, Nath A, Nitrosative stress with HIV dementia causes decreased L-prostaglandin D synthetase activity, Neurology, 70(19-2), 1753-1762, 2007. PMID: 18077799.

  8. Gundry RL, Fu Q,  Jelinek CA, Van Eyk JE, Cotter RJ, Investigation of an Albumin-Enriched Fraction of Human Serum and its Albuminome, Proteomics – Clinical Applications, 1(1), 73-88, 2007. PMID: 20204147. **Article Featured in this Issue

  9. Gundry RL, Allard MW, Moretti TR, Honeycutt RL, Wilson MR, Monson KL, Foran DR, Mitochondrial DNA Analysis of the Domestic Dog: Control Region Variation Within and Among Breeds, Journal of Forensic Sciences, 52(3), 562-572, 2007. PMID: 17456083.

  10. Irani D, Anderson C, Gundry RL Cotter RJ, Moore S, Kerr D, McArthur J, Sacktor N, Pardo C, Jones M, Calabresi P, Nath A, Cleavage of Cystatin C in the CSF of Patients with Multiple Sclerosis, Annals of Neurology, 59(2), 2367-247, 2006. PMID: 16437581.

  11. Gundry RL, Edward R, Kole TP, Sutton C, Cotter RJ, Disposable hydrophobic surface on MALDI targets for enhancing MS and MS/MS data of peptides, Analytical Chemistry, 77(20), 6609-6617, 2005. PMID: 16223247.

  12. Wysong CL, Yokum TS, Morales GA, Gundry RL, ML McLaughlin, RP Hammer, 4-Amino-Piperidine-4-Carboxylic Acid:  A Cyclic α, α -Disubstituted Amino Acid for Preparation of Water-Soluble Highly Helical Peptides,Journal of Organic Chemistry, 61(22), 7650-7651, 1996. PMID: 11667711.

Books, Chapters, Reviews, Perspectives

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+ Book Chapters

  1. Gundry RL, Bioinformatics for Mass Spectrometry based Proteomics, in HIV-1 Proteomics: From Discovery to Clinical Applications, Eds Graham DR and Ott DE. Springer-Verlag, New York, 2016.

  2. Waas M, Farris S, Kropp EM, Beckman JA, Stempien-Otero A, Mahr C, Gundry RL, Stem Cell Proteomics, in Manual of Cardiovascular Proteomics - A Primer for Clinicians, Scientists and Students, Eds Agnetti J, Lindsey M, Foster DB, Ge Y. Springer International Publishing, Switzerland, 2016.

  3. Gundry RL and Cotter RJ, The Albuminome as a Tool for Biomarker Discovery in Clinical Proteomics: from diagnosis to Therapy, Eds JE Van Eyk, MJ Dunn. Wiley, London, 2007.

+ Reviews

  1. Subramanian SP, Gundry RL, The known unknowns of apolipoprotein glycosylation in health and disease, iScience, 25(9):105031, 2022.PMID: 36111253.
  2. Kelly MI, Albahrani M, Castro C, Poon E, Yan B, Littrell J, Waas M, Boheler KR, Gundry RL, Importance of Evaluating Protein Glycosylation in Pluripotent Stem Cell-Derived Cardiomyocytes for Research and Clinical Applications, Pflugers Archiv: European Journal of Physiology, 473(7):1167, 2021. PMID: 33830329.

  1. Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, GUNDRY RL, Stewart S, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS, A high-stringency blueprint of the human proteome. Nature Communications, 11, 5301, 2020. PMID: 33067450.

  2. Boheler KR, Gundry RL, Cell Surface N-Linked Glycoproteins as Potential Stem Cell Markers and Drug Targets, Stem Cells Translational Medicine, 6(1): 131-138, 2016. PMID:28170199.

  3. Mahr C, Gundry RL, Hold or Fold – Proteins in Advanced Heart Failure and Myocardial Recovery, Proteomics – Clinical Applications, 9(1-2): 121-33, 2015. PMID: 25331159.

  4. Muller G, Tarasov KV, GUNDRY RL, Boheler KR, Human ESC/iPSC-based "Omics" and Bioinformatics for Translational Research, Drug Discovery Today: Disease Models, 9(4):e161-e170, 2012. PMID: 23682293.

  5. Gundry RL#, Burridge PW, Boheler KR, Pluripotent Stem Cell Heterogeneity and the Evolving Role of Proteomic Technologies in Stem Cell Biology, Proteomics, 11(20), 3947-61, 2011. PMID: 21834136. #Corresponding author.

  6. Gundry RL, Boheler KR, Van Eyk JE, Wollscheid B, A Novel Role for Proteomics in the Discovery of Cell Surface Markers on Stem Cells: Scratching the Surface, Proteomics - Clinical Applications, 2, 892-903, 2008. PMID: 19526049. **Selected for Journal Cover

  7. Cotter RJ, Iltchenko S, Wang D, Gundry RL Tandem Time-of-Flight (TOF/TOF) Mass Spectrometry and Proteomics, J Mass Spec Society of Japan, 53(1), 7-17, 2005. PMID: 20717501.

  8. Stanley BA#, Gundry RL#, RJ Cotter, Van Eyk JE, Heart disease, clinical proteomics and mass spectrometry, Disease Markers, 20(3), 167-178, 2004. PMID: 15502250. #Denotes equal contribution.

+ Perspectives & Short Communications

  1. Dhawan R, Gundry RL, Brett-Major DM, Mahr C, Thiele GM, Lindsey ML, Anderson DR, COVID-19 and cardiovascular disease: What we know, what we think we konw, and what we need to know. J Molecular and Cellular Cardiology. 144:12-14, 2020.PMID: 32339565.

  2. Waas M, Gundry RLm A call to adopt a ‘fit-for-purpose’ approach to antibody validation for flow cytometry analyses of stem cell models and beyond. Am J Physiol Heart Circ Physiol. Nov 1;317(5):H954-H957, 2019.PMID: 31559827.Listen to the Podcast

+ Editorials

  1. Lindsey M and Gundry RL, Secrets of cardiac remodeling revealed in the secretome. Circulation, 141(20):1645-1647, 2020,PMID:32421415.

  2. Bates ML, Gundry RL, Lindsey ML, Using an Investigative Journalism Approach to Design Mechanistic Experiments in Physiology. Physiology, 35(4):218-219, 2020, PMID: 32490747.

  3. Gundry RL, Van Eyk JE, Unraveling the complexity of circulating forms of Brain Natriuretic Peptide, Clinical Chemistry, 53: 1181 – 1182, 2007. PMID: 17582147.

  4. White MY, Gundry RL, Cordwell SJ, When does a ‘fingerprint’ constitute a diagnostic? Lancet, 368(9540), 971-3, 2006. PMID: 16980095.

+ Books & Journal Issues - Editor

  1. Editors: Boheler KR and Gundry RL, Methods in Molecular Biology: The Surfaceome, Humana Press, Volume 1722, 2018.

  2. Editors: Boheler KR and Gundry RL, Special Issue: Cutting Edge Technology in Cardiovascular Research, Journal of Molecular and Cellular Cardiology, 2020. PMID: 32339568.