2020
Tilburg J, Michaud SA, Maracle CX, Versteeg HH, Borchers CH, van Vlijmen BJM, Mohammed Y. Plasma Protein Signatures of a Murine Venous Thrombosis Model and Slc44a2 Knockout Mice Using Quantitative-Targeted Proteomics. Thromb Haemost. 2020 Mar;120(3):423-436. doi: 10.1055/s-0040-1702229. Epub 2020 Mar 5.
Gaither C, Popp R1, Mohammed Y, Borchers CH. Determination of the concentration range for 267 proteins from 21 lots of commercial human plasma using highly multiplexed multiple reaction monitoring mass spectrometry. Analyst. 2020 Apr 7. doi: 10.1039/c9an01893j. [Epub ahead of print]
Bhardwaj M, Weigl K, Tikk K, Holland-Letz T, Schrotz-King P, Borchers CH, Brenner H. Multiplex quantitation of 270 plasma protein markers to identify a signature for early detection of colorectal cancer. Eur J Cancer. 2020 Jan 20;127:30-40. doi: 10.1016/j.ejca.2019.11.021. [Epub ahead of print]
Shin JJH, Liu P, Chan LJ, Ullah A, Pan J, Borchers CH, Burke JE, Stefan C, Smits GJ, Loewen CJR. pH Biosensing by PI4P Regulates Cargo Sorting at the TGN. pH Biosensing by PI4P Regulates Cargo Sorting at the TGN. Dev Cell. 2020 Jan 9. pii: S1534-5807(19)31031-7. doi: 10.1016/j.devcel.2019.12.010. [Epub ahead of print].
2019
Makepeace KAT, Brodie NI, Popov KI, Gudavicius G, Nelson CJ, Petrotchenko EV, Dokholyan NV, Borchers CH. Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations. J Proteomics. 2019 Nov 1:103544. doi: 10.1016/j.jprot.2019.103544. [Epub ahead of print].
Popov KI, Makepeace KAT, Petrotchenko EV, Dokholyan NV, Borchers CH. Insight into the Structure of the "Unstructured" Tau Protein. Structure. 2019 Oct 14. pii: S0969-2126(19)30309-0. doi: 10.1016/j.str.2019.09.003.
Martínez de Paz A, Khajavi L, Martin H, Claveria-Gimeno R, Tom Dieck S, Cheema MS, Sanchez-Mut JV, Moksa MM, Carles A, Brodie NI, Sheikh TI, Freeman ME, Petrotchenko EV, Borchers CH, Schuman EM, Zytnicki M, Velazquez-Campoy A, Abian O, Hirst M, Esteller M, Vincent JB, Malnou CE, Ausió J. MeCP2-E1 isoform is a dynamically expressed, weakly DNA-bound protein with different protein and DNA interactions compared to MeCP2-E2. Epigenetics Chromatin. 2019 Oct 10;12(1):63. doi: 10.1186/s13072-019-0298-1.
Bhardwaj M, Gies A, Weigl K, Tikk K, Benner A, Schrotz-King P, Borchers CH, Brenner H. Evaluation and Validation of Plasma Proteins Using Two Different Protein Detection Methods for Early Detection of Colorectal Cancer. Cancers (Basel). 2019 Sep 25;11(10). pii: E1426. doi: 10.3390/cancers11101426.
Pires ES, Hardoim CCP, Miranda KR, Secco DA, Lobo LA, de Carvalho DP, Han J, Borchers CH, Ferreira RBR, Salles JF, Domingues RMCP, Antunes LCM. The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon. Front Microbiol. 2019 Sep 4;10:2003. doi: 10.3389/fmicb.2019.02003. eCollection 2019.
2018
Popp R, Li H, Borchers C. 2018 Immuno-MALDI (iMALDI) mass spectrometry for the analysis of proteins in signaling pathways. Expert Rev. Proteomics , 1–8. (doi:10.1080/14789450.2018.1516147)
González Coraspe JA et al. 2018 Biochemical and pathological changes result from mutated Caveolin-3 in muscle. Skelet. Muscle 8, 28. (doi:10.1186/s13395-018-0173-y)
Zahedi RP, Parker CE, Borchers CH. 2018 Immuno-MALDI-TOF-MS in the Clinic. Clin. Chem. 64, 1271–1272. (doi:10.1373/clinchem.2018.292136)
Penn AM et al. 2018 Validation of a proteomic biomarker panel to diagnose minor-stroke and transient ischaemic attack: phase 2 of SpecTRA, a large scale translational study. Biomark. Biochem. Indic. Expo. Response Susceptibility Chem. , 1–11. (doi:10.1080/1354750X.2018.1499130)
Wölter M, Okai CA, Smith DS, Ruß M, Rath W, Pecks U, Borchers CH, Glocker MO. 2018 Maternal Apolipoprotein B100 Serum Levels are Diminished in Pregnancies with Intrauterine Growth Restriction and Differentiate from Controls. Proteomics Clin. Appl. , e1800017. (doi:10.1002/prca.201800017)
Mahdavi S, Jenkins DJA, Borchers CH, El-Sohemy A. 2018 Genetic Variation in 9p21 and the Plasma Proteome. J. Proteome Res. 17, 2649–2656. (doi:10.1021/acs.jproteome.8b00117)
Mnatsakanyan R, Shema G, Basik M, Batist G, Borchers CH, Sickmann A, Zahedi RP. 2018 Detecting post-translational modification signatures as potential biomarkers in clinical mass spectrometry. Expert Rev. Proteomics 15, 515–535. (doi:10.1080/14789450.2018.1483340)
Walter C, Gonczarowska-Jorge H, Sickmann A, Zahedi RP, Meisinger C, Schmidt O. 2018 Advanced tools for the analysis of protein phosphorylation in yeast mitochondria. Anal. Biochem. 554, 23–27. (doi:10.1016/j.ab.2018.05.022)
Bhowmick P, Mohammed Y, Borchers CH. 2018 MRMAssayDB: an integrated resource for validated targeted proteomics assays. Bioinforma. Oxf. Engl. (doi:10.1093/bioinformatics/bty385)
Pett C et al. 2018 Effective Assignment of α2,3/α2,6-Sialic Acid Isomers by LC-MS/MS-Based Glycoproteomics. Angew. Chem. Int. Ed Engl. 57, 9320–9324. (doi:10.1002/anie.201803540)
Nguyen MTN, Shema G, Zahedi RP, Verhelst SHL. 2018 Protease Specificity Profiling in a Pipet Tip Using ‘Charge-Synchronized’ Proteome-Derived Peptide Libraries. J. Proteome Res. 17, 1923–1933. (doi:10.1021/acs.jproteome.8b00004)
Makhoul S, Walter E, Pagel O, Walter U, Sickmann A, Gambaryan S, Smolenski A, Zahedi RP, Jurk K. 2018 Effects of the NO/soluble guanylate cyclase/cGMP system on the functions of human platelets. Nitric Oxide Biol. Chem. 76, 71–80. (doi:10.1016/j.niox.2018.03.008)
Parker CE, Borchers CH. 2018 The Special Issue: Clinical Proteomics for Precision Medicine. Proteomics Clin. Appl. 12. (doi:10.1002/prca.201600144)
Luehr TC, Koide EM, Wang X, Han J, Borchers CH, Helbing CC. 2018 Metabolomic insights into the effects of thyroid hormone on Rana [Lithobates] catesbeiana metamorphosis using whole-body Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging (MALDI-MSI). Gen. Comp. Endocrinol. 265, 237–245. (doi:10.1016/j.ygcen.2018.02.012)
Liu T et al. 2018 Comprehensive bile acid profiling in hereditary intrahepatic cholestasis: Genetic and clinical correlations. Liver Int. Off. J. Int. Assoc. Study Liver 38, 1676–1685. (doi:10.1111/liv.13714)
Kösters M, Leufken J, Schulze S, Sugimoto K, Klein J, Zahedi RP, Hippler M, Leidel SA, Fufezan C. 2018 pymzML v2.0: introducing a highly compressed and seekable gzip format. Bioinforma. Oxf. Engl. 34, 2513–2514. (doi:10.1093/bioinformatics/bty046)
Penn AM et al. 2018 Verification of a proteomic biomarker panel to diagnose minor stroke and transient ischaemic attack: phase 1 of SpecTRA, a large scale translational study. Biomark. Biochem. Indic. Expo. Response Susceptibility Chem. 23, 392–405. (doi:10.1080/1354750X.2018.1434681)
Shema G, Nguyen MTN, Solari FA, Loroch S, Venne AS, Kollipara L, Sickmann A, Verhelst SHL, Zahedi RP. 2018 Simple, scalable, and ultrasensitive tip-based identification of protease substrates. Mol. Cell. Proteomics MCP 17, 826–834. (doi:10.1074/mcp.TIR117.000302)
Perzanowska A, Fatalska A, Wojtas G, Lewandowicz A, Michalak A, Krasowski G, Borchers CH, Dadlez M, Domanski D. 2018 An MRM-Based Cytokeratin Marker Assay as a Tool for Cancer Studies: Application to Lung Cancer Pleural Effusions. Proteomics Clin. Appl. 12. (doi:10.1002/prca.201700084)
Brodie NI, Huguet R, Zhang T, Viner R, Zabrouskov V, Pan J, Petrotchenko EV, Borchers CH. 2018 Top-Down Hydrogen-Deuterium Exchange Analysis of Protein Structures Using Ultraviolet Photodissociation. Anal. Chem. 90, 3079–3082. (doi:10.1021/acs.analchem.7b03655)
Jardim A, Hardie DB, Boitz J, Borchers CH. 2018 Proteomic Profiling of Leishmania donovani Promastigote Subcellular Organelles. J. Proteome Res. 17, 1194–1215. (doi:10.1021/acs.jproteome.7b00817)
Mohammed Y, Pan J, Zhang S, Han J, Borchers CH. 2018 ExSTA: External Standard Addition Method for Accurate High-Throughput Quantitation in Targeted Proteomics Experiments. Proteomics Clin. Appl. 12. (doi:10.1002/prca.201600180)
Eshghi A, Borchers CH. 2018 Multiple Reaction Monitoring Using Double Isotopologue Peptide Standards for Protein Quantification. Methods Mol. Biol. Clifton NJ 1788, 193–214. (doi:10.1007/7651_2017_112)
Urao N, Mirza RE, Corbiere TF, Hollander Z, Borchers CH, Koh TJ. 2017 Thrombospondin-1 and disease progression in dysferlinopathy. Hum. Mol. Genet. 26, 4951–4960. (doi:10.1093/hmg/ddx378)
Han J, Higgins R, Lim MD, Lin K, Yang J, Borchers CH. 2018 Short-Term Stabilities of 21 Amino Acids in Dried Blood Spots. Clin. Chem. 64, 400–402. (doi:10.1373/clinchem.2017.278457)
2017
Gonczarowska-Jorge H, Loroch S, Dell’Aica M, Sickmann A, Roos A, Zahedi RP. 2017 Quantifying Missing (Phospho)Proteome Regions with the Broad-Specificity Protease Subtilisin. Anal. Chem. 89, 13137–13145. (doi:10.1021/acs.analchem.7b02395)
Bowden JA et al. 2017 Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma. J. Lipid Res. 58, 2275–2288. (doi:10.1194/jlr.M079012)
Mohammed Y, van Vlijmen BJ, Yang J, Percy AJ, Palmblad M, Borchers CH, Rosendaal FR. 2017 Multiplexed targeted proteomic assay to assess coagulation factor concentrations and thrombosis-associated cancer. Blood Adv. 1, 1080–1087. (doi:10.1182/bloodadvances.2017007955)
Li H, Popp R, Frohlich B, Chen MX, Borchers CH. 2017 Peptide and Protein Quantification Using Automated Immuno-MALDI (iMALDI). J. Vis. Exp. JoVE (doi:10.3791/55933)
Popp R et al. 2017 Immuno-Matrix-Assisted Laser Desorption/Ionization Assays for Quantifying AKT1 and AKT2 in Breast and Colorectal Cancer Cell Lines and Tumors. Anal. Chem. 89, 10592–10600. (doi:10.1021/acs.analchem.7b02934)
Guarna MM et al. 2017 Peptide biomarkers used for the selective breeding of a complex polygenic trait in honey bees. Sci. Rep. 7, 8381. (doi:10.1038/s41598-017-08464-2)
M Larina I, Percy AJ, Yang J, Borchers CH, M Nosovsky A, I Grigoriev A, N Nikolaev E. 2017 Protein expression changes caused by spaceflight as measured for 18 Russian cosmonauts. Sci. Rep. 7, 8142. (doi:10.1038/s41598-017-08432-w)
Richard VR, Domanski D, Percy AJ, Borchers CH. 2017 An online 2D-reversed-phase - Reversed-phase chromatographic method for sensitive and robust plasma protein quantitation. J. Proteomics 168, 28–36. (doi:10.1016/j.jprot.2017.07.018)
Brodie NI, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH. 2017 Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations. Sci. Adv. 3, e1700479. (doi:10.1126/sciadv.1700479)
LeBlanc A et al. 2017 Multiplexed MRM-Based Protein Quantitation Using Two Different Stable Isotope-Labeled Peptide Isotopologues for Calibration. J. Proteome Res. 16, 2527–2536. (doi:10.1021/acs.jproteome.7b00094)
Li H, Han J, Pan J, Liu T, Parker CE, Borchers CH. 2017 Current trends in quantitative proteomics - an update. J. Mass Spectrom. JMS 52, 319–341. (doi:10.1002/jms.3932)
Reynolds LA et al. 2017 Enteric Helminths Promote Salmonella Coinfection by Altering the Intestinal Metabolome. J. Infect. Dis. 215, 1245–1254. (doi:10.1093/infdis/jix141)
Li H, Popp R, Chen M, MacNamara EM, Juncker D, Borchers CH. 2017 Bead-Extractor Assisted Ready-to-Use Reagent System (BEARS) for Immunoprecipitation Coupled to MALDI-MS. Anal. Chem. 89, 3834–3839. (doi:10.1021/acs.analchem.6b04169)
Mohammed Y et al. 2017 PeptideTracker: A knowledge base for collecting and storing information on protein concentrations in biological tissues. Proteomics 17. (doi:10.1002/pmic.201600210)