Publications – Metabolomics Core Facility

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Structural basis of thiamine transport and drug recognition by SLC19A3.

Gabriel F, Spriestersbach L, Fuhrmann A, Jungnickel KEJ, Mostafavi S, Pardon E, Steyaert J, Löw C

Nature communications, 2024

doi:10.1038/s41467-024-52872-8.

Chemigenetic far-red labels and Ca2+ indicators optimized for photoacoustic imaging.

Cook A, Kaydanov N, Ugarte-Uribe B, Boffi JC, Kamm GB, Prevedel R, Deo C

Journal of the American Chemical Society, 2024

doi:10.1021/jacs.4c07080.

Large-scale evaluation of spatial metabolomics protocols and technologies.

Saharuka V, Vieira LM, Stuart L, Ekelöf M, Molenaar MR, Bailoni A, Ovchinnikova K, Soltwisch J, Bausbacher T, Jakob D, King M, Müller MA, Oetjen J, Pace C, Pinto FE, Strittmatter N, Velickovic D, Spengler B, Muddiman DC, Liebeke M, Janfelt C, Goodwin R, Eberlin LS, Anderton CR, Hopf C, Dreisewerd K, Alexandrov T

bioRxiv, 2024

doi:10.1101/2024.01.29.577354.

In-vivo tracking of deuterium metabolism in mouse organs using LC-MS/MS.

Kasarla SS, Flocke V, Saw NMT, Fecke A, Sickmann A, Gunzer M, Flögel U, Phapale P

Journal of chromatography. A, 2024

doi:10.1016/j.chroma.2024.464691.

Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response.

Ruperti F, Becher I, Stokkermans A, Wang L, Marschlich N, Potel C, Maus E, Stein F, Drotleff B, Schippers KJ, Nickel M, Prevedel R, Musser JM, Savitski MM, Arendt D

Current biology : CB, 2023

doi:10.1016/j.cub.2023.12.021.

NKG2D-mediated detection of metabolically stressed hepatocytes by innate-like T cells is essential for initiation of NASH and fibrosis.

Marinović S, Lenartić M, Mladenić K, Šestan M, Kavazović I, Benić A, Krapić M, Rindlisbacher L, Cokarić Brdovčak M, Sparano C, Litscher G, Turk Wensveen T, Mikolašević I, Fučkar Čupić D, Bilić-Zulle L, Steinle A, Waisman A, Hayday A, Tugues S, Becher B, Polić B, Wensveen FM

Science immunology, 2023

doi:10.1126/sciimmunol.add1599.

A pathogen-specific isotope tracing approach reveals metabolic activities and fluxes of intracellular Salmonella.

Mitosch K, Beyß M, Phapale P, Drotleff B, Nöh K, Alexandrov T, Patil KR, Typas A

PLoS biology, 2023

doi:10.1371/journal.pbio.3002198.

Quantitative analytical and computational workflow for large-scale targeted plasma metabolomics.

Fecke A, Saw NMMT, Kale D, Kasarla SS, Sickmann A, Phapale P

Metabolites, 2023

doi:10.3390/metabo13070844.

Platelet miRNAs: differential expression in coronary artery disease and associations with course of left ventricular systolic function.

Goldschmied A, Drotleff B, Winter S, Schaeffeler E, Schwab M, Gawaz M, Geisler T, Rath D

BMC Cardiovascular Disorders, 2023

doi:10.1186/s12872-023-03362-0.

Mannose is crucial for mesoderm specification and symmetry breaking in gastruloids.

Dingare C, Yang J, Steventon B

bioRxiv, 2023

doi:10.1101/2023.06.05.543730 .

SAM, SAH and C. elegans longevity: insights from a partial AHCY deficiency model.

Pokrzywa W, Thapa P, Banasiak K, Serwa R

npj aging, 2023

doi:10.1038/s41514-023-00125-1.

Large neutral amino acid levels tune perinatal neuronal excitability and survival.

Knaus LS, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler FM, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G

Cell, 2023

doi:10.1016/j.cell.2023.02.037.

A heterotypic assembly mechanism regulates CHIP E3 ligase activity.

Das A, Thapa P, Santiago U, Shanmugam N, Banasiak K, Dąbrowska K, Nolte H, Szulc NA, Gathungu RM, Cysewski D, Krüger M, Dadlez M, Nowotny M, Camacho CJ, Hoppe T, Pokrzywa W

The EMBO journal, 2022

doi:10.15252/embj.2021109566.

Coupling proteomics and metabolomics for the unsupervised identification of protein-metabolite interactions in Chaetomium thermophilum.

Li Y, Kuhn M, Zukowska-Kasprzyk J, Hennrich ML, Kastritis PL, O'Reilly FJ, Phapale P, Beck M, Gavin AC, Bork P

PloS one, 2021

doi:10.1371/journal.pone.0254429.

Quantification reveals early dynamics in Drosophila maternal gradients.

Shlemov A, Alexandrov T, Golyandina N, Holloway D, Baumgartner S, Spirov AV

PloS one, 2021

doi:10.1371/journal.pone.0244701.

High-throughput functional characterization of protein phosphorylation sites in yeast.

Viéitez C, Busby BP, Ochoa D, Mateus A, Memon D, Galardini M, Yildiz U, Trovato M, Jawed A, Geiger AG, Oborská-Oplová M, Potel CM, Vonesch SC, Szu Tu C, Shahraz M, Stein F, Steinmetz LM, Panse VG, Noh KM, Savitski MM, Typas A, Beltrao P

Nature biotechnology, 2021

doi:10.1038/s41587-021-01051-x.

Rapid automated annotation and analysis of N-glycan mass spectrometry imaging data sets using NGlycDB in METASPACE.

Veličković D, Bečejac T, Mamedov S, Sharma K, Ambalavanan N, Alexandrov T, Anderton CR

Analytical chemistry, 2021

doi:10.1021/acs.analchem.1c02347.

Bioaccumulation of therapeutic drugs by human gut bacteria.

Klünemann M, Andrejev S, Blasche S, Mateus A, Phapale P, Devendran S, Vappiani J, Simon B, Scott TA, Kafkia E, Konstantinidis D, Zirngibl K, Mastrorilli E, Banzhaf M, Mackmull MT, Hövelmann F, Nesme L, Brochado AR, Maier L, Bock T, Periwal V, Kumar M, Kim Y, Tramontano M, Schultz C, Beck M, Hennig J, Zimmermann M, Sévin DC, Cabreiro F, Savitski MM, Bork P, Typas A, Patil KR

Nature, 2021

doi:10.1038/s41586-021-03891-8.

Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion.

Konstantinidis D, Pereira F, Geissen EM, Grkovska K, Kafkia E, Jouhten P, Kim Y, Devendran S, Zimmermann M, Patil KR

Molecular systems biology, 2021

doi:10.15252/msb.202010189.

Metabolic decisions in development and disease-a Keystone Symposia report.

Cable J, Pourquié O, Wellen KE, Finley LWS, Aulehla A, Gould AP, Teleman A, Tu WB, Garrett WS, Miguel-Aliaga I, Perrimon N, Hooper LV, Walhout AJM, Wei W, Alexandrov T, Erez A, Ralser M, Rabinowitz JD, Hemalatha A, Gutiérrez-Pérez P, Chandel NS, Rutter J, Locasale JW, Landoni JC, Christofk H

Annals of the New York Academy of Sciences, 2021

doi:10.1111/nyas.14678.

Facilitating imaging mass spectrometry of microbial specialized metabolites with METASPACE.

Nguyen DD, Saharuka V, Kovalev V, Stuart L, Del Prete M, Lubowiecka K, De Mot R, Venturi V, Alexandrov T

Metabolites, 2021

doi:10.3390/metabo11080477.

Structural basis of human separase regulation by securin and CDK1-cyclin B1.

Yu J, Raia P, Ghent CM, Raisch T, Sadian Y, Cavadini S, Sabale PM, Barford D, Raunser S, Morgan DO, Boland A

Nature, 2021

doi:10.1038/s41586-021-03764-0.

SpaceM reveals metabolic states of single cells.

Rappez L, Stadler M, Triana S, Gathungu RM, Ovchinnikova K, Phapale P, Heikenwalder M, Alexandrov T

Nature methods, 2021

doi:10.1038/s41592-021-01198-0.

Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection.

Triana S, Stanifer ML, Metz-Zumaran C, Shahraz M, Mukenhirn M, Kee C, Serger C, Koschny R, Ordonez-Rueda D, Paulsen M, Benes V, Boulant S, Alexandrov T

Molecular Systems Biology , 2021

doi:10.15252/msb.20209833.

Structure of the mycobacterial ESX-5 type VII secretion system pore complex.

Beckham KSH, Ritter C, Chojnowski G, Ziemianowicz DS, Mullapudi E, Rettel M, Savitski MM, Mortensen SA, Kosinski J, Wilmanns M

Science advances, 2021

doi:10.1126/sciadv.abg9923.

Single-cell analyses reveal SARS-CoV-2 interference with intrinsic immune response in the human gut.

Triana S, Metz-Zumaran C, Ramirez C, Kee C, Doldan P, Shahraz M, Schraivogel D, Gschwind AR, Sharma AK, Steinmetz LM, Herrmann C, Alexandrov T, Boulant S, Stanifer ML

Molecular systems biology, 2021

doi:10.15252/msb.202110232.

Adaptive pixel mass recalibration for mass spectrometry imaging based on locally endogenous biological signals.

La Rocca R, Kune C, Tiquet M, Stuart L, Eppe G, Alexandrov T, De Pauw E, Quinton L

Analytical chemistry, 2021

doi:10.1021/acs.analchem.0c05071.

Public LC-Orbitrap tandem mass spectral library for metabolite identification.

Phapale P, Palmer A, Gathungu RM, Kale D, Brügger B, Alexandrov T

Journal of proteome research, 2021

doi:10.1021/acs.jproteome.0c00930.

amTCO, a new trans-cyclooctene derivative to study drug-target interactions in cells.

Echalier C, Rutkowska A, Kojic A, Thomson DW, Edwards LJ, McKay BSJ, Mülbaier M, Schultz C, Bergamini G

Chemical communications, 2021

doi:10.1039/d0cc06709a.

An integrated multiomic and quantitative label-free microscopy-based approach to study pro-fibrotic signalling in ex vivo human precision-cut lung slices.

Khan MM, Poeckel D, Halavatyi A, Zukowska-Kasprzyk J, Stein F, Vappiani J, Sevin DC, Tischer C, Zinn N, Eley JD, Gudmann NS, Muley T, Winter H, Fisher AJ, Nanthakumar CB, Bergamini G, Pepperkok R

The European respiratory journal, 2020

doi:10.1183/13993003.00221-2020.

The functional proteome landscape of Escherichia coli.

Mateus A, Hevler J, Bobonis J, Kurzawa N, Shah M, Mitosch K, Goemans CV, Helm D, Stein F, Typas A, Savitski MM

Nature, 2020

doi:10.1038/s41586-020-3002-5.

Feature-based molecular networking in the GNPS analysis environment.

Nothias LF, Petras D, Schmid R, Dührkop K, Rainer J, Sarvepalli A, Protsyuk I, Ernst M, Tsugawa H, Fleischauer M, Aicheler F, Aksenov AA, Alka O, Allard PM, Barsch A, Cachet X Caraballo-Rodriguez AM, Da Silva RR , Dang T, Garg N, Gauglitz JM, Gurevich A, Isaac G, Jarmusch AK, Kameník Z, Kang KB, Kessler N, Koester I, Korf A, Le Gouellec A, Ludwig M, Martin HC, McCall LI, McSayles J, Meyer SW, Mohimani H, Morsy M, Moyone O, Neumann S, Neuweger H, Nguyen NH, Nothias-Esposito M, Paolini J, Phelan VV, Pluskal T, Quinn RA, Rogers S, Shrestha B, Tripathi A, van der Hooft JJJ, Vargas F, Weldon KC, Witting M, Yang H, Zhang Z, Zubeil F, Kohlbacher O, Böcker S, Alexandrov T, Bandeira N, Wang M, Dorrestein PC

Nature methods, 2020

doi:10.1038/s41592-020-0933-6.

Storage conditions of human kidney tissue sections affect spatial lipidomics analysis reproducibility.

Lukowski JK, Pamreddy A, Velickovic D, Zhang G, Pasa-Tolic L, Alexandrov T, Sharma K, Anderton CR, Kidney Precision Medicine Project

Journal of the American Society for Mass Spectrometry, 2020

doi:10.1021/jasms.0c00256.

Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project.

Ong E, Wang LL, Schaub J, O'Toole JF, Steck B, Rosenberg AZ, Dowd F, Hansen J, Barisoni L, Jain S, de Boer IH, Valerius MT, Waikar SS, Park C, Crawford DC, Alexandrov T, Anderton CR, Stoeckert C, Weng C, Diehl AD, Mungall CJ, Haendel M, Robinson PN, Himmelfarb J, Iyengar R, Kretzler M, Mooney S, He Y, Kidney Precision Medicine Project

Nature reviews. Nephrology, 2020

doi:10.1038/s41581-020-00335-w.

Untargeted metabolomics workshop report: quality control considerations from sample preparation to data analysis.

Phapale P, Rai V, Mohanty AK, Srivastava S

Journal of the American Society for Mass Spectrometry, 2020

doi:10.1021/jasms.0c00224.

Spatial metabolomics and imaging mass spectrometry in the age of artificial intelligence.

Alexandrov T

Annual review of biomedical data science, 2020

doi:10.1146/annurev-biodatasci-011420-031537.

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.

Li Y, Kuhn M, Gavin AC, Bork P

Bioinformatics (Oxford, England), 2019

doi:10.1093/bioinformatics/btz736.

GPD1 specifically marks dormant glioma stem cells with a distinct metabolic profile.

Rusu P, Shao C, Neuerburg A, Acikgöz AA, Wu Y, Zou P, Phapale P, Shankar TS, Döring K, Dettling S, Körkel-Qu H, Bekki G, Costa B, Guo T, Friesen O, Schlotter M, Heikenwalder M, Tschaharganeh DF, Bukau B, Kramer G, Angel P, Herold-Mende C, Radlwimmer B, Liu HK

Cell Stem Cell, 2019

doi:10.1016/j.stem.2019.06.004.

The RNA-binding protein YBX3 controls amino acid levels by regulating SLC mRNA abundance.

Cooke A, Schwarzl T, Huppertz I, Kramer G, Mantas P, Alleaume AM, Huber W, Krijgsveld J, Hentze MW

Cell reports, 2019

doi:10.1016/j.celrep.2019.05.039.

Clearance by microglia depends on packaging of phagosomes into a unique cellular compartment.

Villani A, Benjaminsen J, Moritz C, Henke K, Hartmann J, Norlin N, Richter K, Schieber NL, Franke T, Schwab Y, Peri F

Developmental cell, 2019

doi:10.1016/j.devcel.2019.02.014.

Spatial single-cell profiling of intracellular metabolomes in situ.

Rappez L, Stadler M, Triana S, Phapale P, Heikenwalder M, Alexandrov T

biorxiv, 2019

doi:10.1101/510222.

Endogenous fatty acids are essential signaling factors of pancreatic β-cells and insulin secretion.

Hauke S, Keutler K, Phapale P, Yushchenko DA, Schultz C

Diabetes, 2018

doi:10.2337/db17-1215.

Creating a 3D microbial and chemical snapshot of a human habitat.

Kapono CA, Morton JT, Bouslimani A, Melnik AV, Orlinsky K, Knaan TL, Garg N, Vázquez-Baeza Y, Protsyuk I, Janssen S, Zhu Q, Alexandrov T, Smarr L, Knight R, Dorrestein PC

Scientific reports, 2018

doi:10.1038/s41598-018-21541-4.

3D molecular cartography using LC-MS facilitated by Optimus and 'ili software.

Protsyuk I, Melnik AV, Nothias LF, Rappez L, Phapale P, Aksenov AA, Bouslimani A, Ryazanov S, Dorrestein PC, Alexandrov T

Nature protocols, 2018

doi:10.1038/nprot.2017.122.

Curatr: a web application for creating, curating, and sharing a mass spectral library.

Palmer A, Phapale P, Fay D, Alexandrov T

Bioinformatics , 2017

doi:10.1093/bioinformatics/btx786.

Metabolic shifts in residual breast cancer drive tumor recurrence

Havas KM, Milchevskaya V, Radic K, Alladin A, Kafkia E, Garcia M, Stolte J, Klaus B, Rotmensz N, Gibson TJ, Burwinkel B, Schneeweiss A, Pruneri G, Patil KR, Sotillo R, Jechlinger M

The Journal of clinical investigation, 2017

doi:10.1172/JCI89914.

Structure of p300 in complex with acyl-CoA variants.

Kaczmarska Z, Ortega E, Goudarzi A, Huang H, Kim S, Márquez JA, Zhao Y, Khochbin S, Panne D

Nature Chemical Biology, 2017

doi:10.1038/nchembio.2217.

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry.

Palmer A, Phapale P, Chernyavsky I, Lavigne R, Fay D, Tarasov A, Kovalev V, Fuchser J, Nikolenko S, Pineau C, Becker M, Alexandrov T

Nature methods, 2017

doi:10.1038/nmeth.4072.

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, Boya P CA, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJ, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AM, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BØ, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N

Nature biotechnology, 2016

doi:10.1038/nbt.3597.