Publications
Read our recent publications and research papers
Explore detailed insights into our technology through the publications authored by the MSAID team:
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Preprint: Unifying the analysis of bottom-up proteomics data with CHIMERYS
Martin Frejno, Michelle T. Berger, Johanna Tüshaus, et. al. bioRxiv 2024.05.27.596040; DOI: https://doi.org/10.1101/2024.05.27.596040
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INFERYS rescoring: Boosting peptide identifications and scoring confidence of database search results
Daniel P. Zolg, Siegfried Gessulat, Carmen Paschke, et. al. Rapid Commun Mass Spectrom. 2021 May. ;e9128.
DOI: https://doi.org/10.1002/rcm.9128
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Repurposed 3D Printer Allows Economical and Programmable Fraction Collection for Proteomics of Nanogram Scale Samples
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Shotgun Proteomics Links Proteoglycan-4+ Extracellular Vesicles to Cognitive Protection in Amyotrophic Lateral Sclerosis
DOI: https://doi.org/10.3390/biom14060727. PMID: 38927130; PMCID: PMC11202157.
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Liver and pancreatic-targeted interleukin-22 as a therapeutic for metabolic dysfunction-associated steatohepatitis
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Deciphering Early and Progressive Molecular Signatures in Alzheimer’s Disease through Integrated Longitudinal Proteomic and Pathway Analysis in a Rodent Model
DOI: https://doi.org/10.3390/ijms25126469. PMID: 38928172; PMCID: PMC11203991.
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A blood-brain barrier-penetrant AAV gene therapy improves neurological function in symptomatic mucolipidosis IV mice
DOI: https://doi.org/10.1016/j.omtm.2024.101269. PMID: 38934011; PMCID: PMC11201152.
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Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications
DOI: https://doi.org/10.1038/s41467-024-45391-z
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Extracellular Vesicle Protein Expression in Doped Bioactive Glasses: Further Insights Applying Anomaly Detection
PMID: 38542533; PMCID: PMC10971221.
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Proteome and Dihydrorhodamine Profiling of Bronchoalveolar Lavage in Patients with Chronic Pulmonary Aspergillosis
PMID: 38786669; PMCID: PMC11122433.
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The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes
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Differential proteomics profile of microcapillary networks in response to sound pattern-driven local cell density enhancement
DOI: https://doi.org/10.1016/j.bbiosy.2024.100094. PMID: 38596510; PMCID: PMC11001772.
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Differential temporal release and lipoprotein loading in B. thetaiotaomicron bacterial extracellular vesicles
PMID: 38240185; PMCID: PMC10797578.
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A CPF-like phosphatase module links transcription termination to chromatin silencing
Epub 2024 Jun 7. PMID: 38851185; PMCID: PMC7616277.
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Rab30 facilitates lipid homeostasis during fasting
DOI: https://doi.org/10.1038/s41467-024-48959-x
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The Deep Proteomics Approach Identified Extracellular Vesicular Proteins Correlated to Extracellular Matrix in Type One and Two Endometrial Cancer
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Brain cell type specific proteomics approach to discover pathological mechanisms in the childhood CNS disorder mucolipidosis type IV
DOI: https://doi.org/10.3389/fnmol.2023.1215425. PMID: 37609073; PMCID: PMC10440433.
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Label-free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing
Epub 2023 Mar 1. PMID: 36806919; PMCID: PMC10909491.
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An Automated Nanowell-Array Workflow for Quantitative Multiplexed Single-Cell Proteomics Sample Preparation at High Sensitivity
DOI: https://doi.org/10.1016/j.mcpro.2023.100665. Epub 2023 Oct 14. PMID: 37839701; PMCID: PMC10684380.
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Evidence of a role for CutRS and actinorhodin in the secretion stress response in Streptomyces coelicolor M145
PMID: 37418299; PMCID: PMC10433416.
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Data-Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label-Free Single-Cell Proteomics
DOI: https://doi.org/10.1002/anie.202303415
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Robust and Easy-to-Use One-Pot Workflow for Label-Free Single-Cell Proteomics
DOI: https://pubs.acs.org/doi/full/10.1021/acs.analchem.2c05022
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VAL1 acts as an assembly platform co-ordinating co-transcriptional repression and chromatin regulation at Arabidopsis FLC
Mikulski, P., Wolff, P., Lu, T. et al. VAL1 acts as an assembly platform co-ordinating co-transcriptional repression and chromatin regulation at Arabidopsis FLC. Nat Commun 13, 5542 (2022). DOI: https://doi.org/10.1038/s41467-022-32897-7
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Comparative Evaluation of Proteome Discoverer and FragPipe for the TMT-Based Proteome Quantification
He T, Liu Y, Zhou Y, Li L, Wang H, Chen S, Gao J, Jiang W, Yu Y, Ge W, Chang HY, Fan Z, Nesvizhskii AI, Guo T, Sun Y. Comparative Evaluation of Proteome Discoverer and FragPipe for the TMT-Based Proteome Quantification. J Proteome Res. 2022 Dec 2;21(12):3007-3015.
DOI: https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00390. Epub 2022 Oct 31. PMID: 36315902.
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ProteomicsML: An Online Platform for Community-Curated Datasets and Tutorials for Machine Learning in Proteomics
Tobias Greisager Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, et al. October 2022. ChemRxiv.
DOI: https://chemrxiv.org/engage/chemrxiv/article-details/633c51a2ea6a223bde08c5df
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Coupling High-Field Asymmetric Ion Mobility Spectrometry with Capillary Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry Improves Protein Identifications in Bottom-Up Proteomic Analysis of Low Nanogram Samples
Kendall R. Johnson, Michal Greguš, and Alexander R. Ivanov. J. Proteome Res. 2022, 21, 10, 2453–2461.
DOI: https://doi.org/10.1021/acs.jproteome.2c00337.
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Deep Single-Shot NanoLC-MS Proteome Profiling with a 1500 Bar UHPLC System, Long Fully Porous Columns, and HRAM MS
Runsheng Z., Karel S., Christopher Pynn, et al. J. Proteome Res. 2022 Sept. DOI: https://doi.org/10.1021/acs.jproteome.2c00270.
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Single-Cell Proteome Profiling of Neuronal Cells
Misal, S.A., Kelly, R.T. (2022). In: Sweedler, J.V., Eberwine, J., Fraser, S.E. (eds) Single Cell ‘Omics of Neuronal Cells. Neuromethods, vol 184. Humana, New York, NY. DOI: https://doi.org/10.1007/978-1-0716-2525-5_3
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Development of Highly Sensitive LC–MS and CE–MS Methods for In-Depth Proteomic and Glycomic Profiling of Limited Biological Samples
August 1, 2022. Michal Gregus, Alan Zimmerman, Anne-Lise Marie, Kendall R. Johnson, Alexander R. Ivanov
LCGC North America, August 2022, Volume 40, Issue 8. Pages: 393–397
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In-Depth Mass Spectrometry-Based Proteomics of Formalin-Fixed, Paraffin-Embedded Tissues with a Spatial Resolution of 50–200 μm
Andikan J. Nwosu, Santosh A. Misal, Thy Truong, et al. J. Proteome Res. 2022 Aug.
DOI: https://doi.org/10.1021/acs.jproteome.2c00409.
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Protein SUMOylation is a sex-specific regulator of fear memory formation in the amygdala
Aspen Gustin, Shaghayegh Navabpour, KaylaFarrella, et al. 2022 Jul. DOI: https://doi.org/10.1016/j.bbr.2022.113928.
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Label-Free Profiling of up to 200 Single-Cell Proteomes per Day Using a Dual-Column Nanoflow Liquid Chromatography Platform
Kei G. I. Webber, Thy Truong, S. Madisyn Johnston, et al. Anal. Chem. 2022 Apr. 94, 15, 6017–6025.
DOI: https://doi.org/10.1021/acs.analchem.2c00646.
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Capillary Electrophoresis Coupled to Electrospray Ionization Tandem Mass Spectrometry for Ultra-Sensitive Proteomic Analysis of Limited Samples
Kendall R. Johnson, Michal Greguš, James C. Kostas, and Alexander R. Ivanov. Anal. Chem. 2022, 94, 2, 704–713. Jan 2022.
DOI: https://doi.org/10.1021/acs.analchem.1c02929.
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Proteomic Analysis Reveals Sex-Specific Protein Degradation Targets in the Amygdala During Fear Memory Formation
Farrell K, Musaus M, Navabpour S, et al. Front. Mol. Neurosci. 2021 Sept. 14:716284.
DOI: https://doi.org/10.3389/fnmol.2021.716284.
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Ultrasensitive NanoLC-MS of Subnanogram Protein Samples Using Second Generation Micropillar Array LC Technology with Orbitrap Exploris 480 and FAIMS PRO
DOI: https://doi.org/10.1021/acs.analchem.1c00990.
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Proteome Discoverer - A Community Enhanced Data Processing Suite for Protein Informatics