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Read our recent publications and research papers

Explore detailed insights into our technology through the publications authored by the MSAID team:

  • Unifying the analysis of bottom-up proteomics data with CHIMERYS

Frejno, M., Berger, M.T., Tüshaus, J. et al. Unifying the analysis of bottom-up proteomics data with CHIMERYS. Nat Methods (2025)
DOI: https://doi.org/10.1038/s41592-025-02663-w

  • A Scalable, Web-Based Platform for Proteomics Data Processing, Result Storage and Analysis

Markus Schneider, Daniel P. Zolg, Patroklos Samaras, et al. Journal of Proteome Research Article ASAP.
DOI: https://pubs.acs.org/doi/10.1021/acs.jproteome.4c00871

  • 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

  • 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

Recent publications featuring MSAID Software

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Collection of articles from scientists and professionals who incorporate INFERYS, INFERYS Rescoring, or CHIMERYS technologies for their research

Year of publication: 2025 | 2024 | 2023 | 2022 | 2021


2025

  • Proteomic Characterization of Cardioprotective Human Acellular Amniotic Fluid

Ryan Bia, Grace Mitchell, Hadi Javan, Ian Nickel, Jan Pierce, Craig H. Selzman, and Sarah Franklin. Proteomic Characterization of Cardioprotective Human Acellular Amniotic Fluid. ACS Omega Article ASAP. DOI: https://doi.org/10.1021/acsomega.4c09451

  • Metabolically activated and highly polyfunctional intratumoral VISTA+ regulatory B cells are associated with tumor recurrence in early-stage NSCLC

Lo Tartaro, D., Aramini, B., Masciale, V. et al. Metabolically activated and highly polyfunctional intratumoral VISTA+ regulatory B cells are associated with tumor recurrence in early-stage NSCLC. Mol Cancer 24, 16 (2025). DIO: https://doi.org/10.1186/s12943-024-02209-2

  • A Pilot Study of Exosome Proteomic Profiling Reveals Dysregulated Metabolic Pathways in Endometrial Cancer

Kharrat, F., Capaci, V., Conti, A., et al. (2025). A Pilot Study of Exosome Proteomic Profiling Reveals Dysregulated Metabolic Pathways in Endometrial Cancer. Biomedicines, 13(1), 95. DOI: https://doi.org/10.3390/biomedicines13010095

  • Review and Practical Guide for Getting Started With Single-Cell Proteomics

Hsien-Jung L. Lin, Kei G. I. Webber, Andikan J. Nwosu, and Ryan T. Kelly. Review and Practical Guide for Getting Started With Single-Cell Proteomics. Proteomics 25, no. 1-2 (2025): e202400021. DOI: https://doi.org/10.1002/pmic.202400021.


2024

  • Rebalancing the seed proteome following deletion of vicilin-related genes in pea (Pisum sativum L.)

Tracey Rayner, Gerhard Saalbach, Martin Vickers, et al. Rebalancing the seed proteome following deletion of vicilin-related genes in pea (Pisum sativum L.), Journal of Experimental Botany, 2024;, erae518. DOI: https://doi.org/10.1093/jxb/erae518

  • A blood-brain barrier-penetrant AAV gene therapy improves neurological function in symptomatic mucolipidosis IV mice

Sangster, Madison L. et al. Molecular Therapy Methods & Clinical Development, Volume 32, Issue 2, 101269
DOI: https://doi.org/10.1016/j.omtm.2024.101269

  • B-146 Unlocking the potential of large-cohort proteomics studies with the Orbitrap Astral mass platform 

Y Xuan, A Pashkova, M Zeller, C T Wirth, et all. B-146 Unlocking the potential of large-cohort proteomics studies with the Orbitrap Astral mass platform, Clinical Chemistry, Volume 70, Issue Supplement_1, October 2024, hvae106.506. DOI: https://doi.org/10.1093/clinchem/hvae106.506

  • Repurposed 3D Printer Allows Economical and Programmable Fraction Collection for Proteomics of Nanogram Scale Samples

Eduardo S. Kitano, Gareth Nisbet, Yana Demyanenko, et al. Repurposed 3D Printer Allows Economical and Programmable Fraction Collection for Proteomics of Nanogram Scale Samples. Anal. Chem (2024). DOI: https://pubs.acs.org/doi/10.1021/acs.analchem.4c01731

  • Applying UHPLC-HRAM MS/MS Method to Assess Host Cell Protein Clearance during the Purification Process Development of Therapeutic mAbs

Kiyonami, R., Melani, R., Chen, Y., Leon, A. D., & Du, M. (2024). Applying UHPLC-HRAM MS/MS Method to Assess Host Cell Protein Clearance during the Purification Process Development of Therapeutic mAbs. International Journal of Molecular Sciences, 25(17), 9687.
DOI: https://doi.org/10.3390/ijms25179687

  • Shotgun Proteomics Links Proteoglycan-4+ Extracellular Vesicles to Cognitive Protection in Amyotrophic Lateral Sclerosis

Vilardo B, De Marchi F, Raineri D, Manfredi M, et al.  A. Shotgun Proteomics Links Proteoglycan-4+ Extracellular Vesicles to Cognitive Protection in Amyotrophic Lateral Sclerosis. Biomolecules. 2024 Jun 19;14(6):727. DOI: https://doi.org/10.3390/biom14060727.
PMID: 38927130; PMCID: PMC11202157.

  • Activity of Various Cathepsin Proteases and Enrichment of Klotho Protein in the Urine and Urinary Extracellular Vesicles After SARS-CoV-2 Infection

Bala, N., Rafay, R. H., Glover, S. C., & Alli, A. A. (2025). Activity of Various Cathepsin Proteases and Enrichment of Klotho Protein in the Urine and Urinary Extracellular Vesicles After SARS-CoV-2 Infection. Viruses, 17(1), 25. DOI: https://doi.org/10.3390/v17010025

  • Liver and pancreatic-targeted interleukin-22 as a therapeutic for metabolic dysfunction-associated steatohepatitis

Sajiir, H., Keshvari, S., Wong, K.Y., et al. Liver and pancreatic-targeted interleukin-22 as a therapeutic for metabolic dysfunction-associated steatohepatitis. Nat Commun 15, 4528 (2024). DOI: https://doi.org/10.1038/s41467-024-48317-x

  • Deciphering Early and Progressive Molecular Signatures in Alzheimer’s Disease through Integrated Longitudinal Proteomic and Pathway Analysis in a Rodent Model

Yadikar H, Ansari MA, Abu-Farha M, Joseph S, Thomas BT, Al-Mulla F. Deciphering Early and Progressive Molecular Signatures in Alzheimer's Disease through Integrated Longitudinal Proteomic and Pathway Analysis in a Rodent Model. Int J Mol Sci. 2024 Jun 12;25(12):6469.
DOI: https://doi.org/10.3390/ijms25126469. PMID: 38928172; PMCID: PMC11203991.

  • A blood-brain barrier-penetrant AAV gene therapy improves neurological function in symptomatic mucolipidosis IV mice

Sangster ML, Bishop MM, Yao Y, Feitor JF, Shahriar S, Miller ME, Chekuri AK, Budnik B, Bei F, Grishchuk Y. A blood-brain barrier-penetrant AAV gene therapy improves neurological function in symptomatic mucolipidosis IV mice. Mol Ther Methods Clin Dev. 2024 May 21;32(2):101269.
DOI: https://doi.org/10.1016/j.omtm.2024.101269. PMID: 38934011; PMCID: PMC11201152.

  • Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications

Matzinger, M., Schmücker, A., Yelagandula, R. et al. Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications. Nat Commun 15, 1019 (2024).
DOI: https://doi.org/10.1038/s41467-024-45391-z

  • Extracellular Vesicle Protein Expression in Doped Bioactive Glasses: Further Insights Applying Anomaly Detection

Nascimben M, Abreu H, Manfredi M, Cappellano G, Chiocchetti A, Rimondini L. Extracellular Vesicle Protein Expression in Doped Bioactive Glasses: Further Insights Applying Anomaly Detection. Int J Mol Sci. 2024 Mar 21;25(6):3560. doi: https://doi.org/10.3390/ijms25063560.
PMID: 38542533; PMCID: PMC10971221.

  • Proteome and Dihydrorhodamine Profiling of Bronchoalveolar Lavage in Patients with Chronic Pulmonary Aspergillosis

Assing K, Laursen CB, Campbell AJ, Beck HC, Davidsen JR. Proteome and Dihydrorhodamine Profiling of Bronchoalveolar Lavage in Patients with Chronic Pulmonary Aspergillosis. J Fungi (Basel). 2024 Apr 25;10(5):314. DOI: https://doi.org/10.3390/jof10050314.
PMID: 38786669; PMCID: PMC11122433.

  • The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes

Dumas, T., Martinez Pinna, R., Lozano, C. et al. The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes. Microbiome 12, 46 (2024). DOI: https://doi.org/10.1186/s40168-024-01766-4

  • B-148 Bacer: decentralized isotope dilution method with lab blinding for blood alcohol content

M Nie, X Li, W Xiong, X Zou, B Zheng, B-148 Bacer: decentralized isotope dilution method with lab blinding for blood alcohol content, Clinical Chemistry, Volume 70, Issue Supplement_1, October 2024, hvae106.508, DOI: https://doi.org/10.1093/clinchem/hvae106.508

  • Differential proteomics profile of microcapillary networks in response to sound pattern-driven local cell density enhancement

Di Marzio N, Tognato R, Bella ED, De Giorgis V, Manfredi M, Cochis A, Alini M, Serra T. Differential proteomics profile of microcapillary networks in response to sound pattern-driven local cell density enhancement. Biomater Biosyst. 2024 Mar 29;14:100094.
DOI: https://doi.org/10.1016/j.bbiosy.2024.100094. PMID: 38596510; PMCID: PMC11001772.

  • Thermal inkjet makes label-free single-cell proteomics accessible and easy

Stanisheuski S, Ebrahimi A, Vaidya KA, Jang HS, Yang L, Eddins AJ, Marean-Reardon C, Franco MC and Maier CS (2024) Thermal inkjet makes label-free single-cell proteomics accessible and easy. Front. Chem. 12:1428547. DOI: https://doi.org/10.3389/fchem.2024.1428547

  • Efficient and Sensitive Sample Preparation, Separations, and Data Acquisition for Label-Free Single-Cell Proteomics

Truong, T., Sanchez-Avila, X., Webber, K.G.I., Johnston, S.M., Kelly, R.T. (2024). Efficient and Sensitive Sample Preparation, Separations, and Data Acquisition for Label-Free Single-Cell Proteomics. In: Vegvari, A., Teppo, J., Zubarev, R.A. (eds) Mass Spectrometry Based Single Cell Proteomics. Methods in Molecular Biology, vol 2817. Humana, New York, NY. DOI: https://doi.org/10.1007/978-1-0716-3934-4_7

  • Differential temporal release and lipoprotein loading in B. thetaiotaomicron bacterial extracellular vesicles

Juodeikis R, Martins C, Saalbach G, Richardson J, Koev T, Baker DJ, Defernez M, Warren M, Carding SR. Differential temporal release and lipoprotein loading in B. thetaiotaomicron bacterial extracellular vesicles. J Extracell Vesicles. 2024 Jan;13(1):e12406. DIO: https://doi.org/10.1002/jev2.12406.
PMID: 38240185; PMCID: PMC10797578.

  • A CPF-like phosphatase module links transcription termination to chromatin silencing

Mateo-Bonmatí E, Montez M, Maple R, Fiedler M, Fang X, Saalbach G, Passmore LA, Dean C. A CPF-like phosphatase module links transcription termination to chromatin silencing. Mol Cell. 2024 Jun 20;84(12):2272-2286.e7. DOI: https://doi.org/10.1016/j.molcel.2024.05.016.
Epub 2024 Jun 7. PMID: 38851185; PMCID: PMC7616277.

  • In Drosophila Hemolymph, Serine Proteases Are the Major Gelatinases and Caseinases

Gatti, J.-L., Lemauf, S., Belghazi, M., Arthaud, L., & Poirié, M. (2024). In Drosophila Hemolymph, Serine Proteases Are the Major Gelatinases and Caseinases. Insects, 15(4), 234. DOI: https://doi.org/10.3390/insects15040234

  • Rab30 facilitates lipid homeostasis during fasting

Smith, D.M., Liu, B.Y. & Wolfgang, M.J. Rab30 facilitates lipid homeostasis during fasting. Nat Commun 15, 4469 (2024). 
DOI: https://doi.org/10.1038/s41467-024-48959-x

  • The Deep Proteomics Approach Identified Extracellular Vesicular Proteins Correlated to Extracellular Matrix in Type One and Two Endometrial Cancer

Capaci, V.; Kharrat, F.; Conti, A.; Salviati, E.; Basilicata, M.G.; Campiglia, P.; Balasan, N.; Licastro, D.; Caponnetto, F.; Beltrami, A.P.; et al. The Deep Proteomics Approach Identified Extracellular Vesicular Proteins Correlated to Extracellular Matrix in Type One and Two Endometrial Cancer. Int. J. Mol. Sci. 2024, 25, 4650. DOI: https://doi.org/10.3390/ijms25094650


2023

  • Brain cell type specific proteomics approach to discover pathological mechanisms in the childhood CNS disorder mucolipidosis type IV

Sangster M, Shahriar S, Niziolek Z, Carisi MC, Lewandowski M, Budnik B, Grishchuk Y. Brain cell type specific proteomics approach to discover pathological mechanisms in the childhood CNS disorder mucolipidosis type IV. Front Mol Neurosci. 2023 Aug 7;16:1215425. 
DOI: https://doi.org/10.3389/fnmol.2023.1215425. PMID: 37609073; PMCID: PMC10440433.

  • Label-free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing

Matzinger M, Mayer RL, Mechtler K. Label-free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing. Proteomics. 2023 Jul;23(13-14):e2200162. DOI: https://doi.org/10.1002/pmic.202200162.
Epub 2023 Mar 1. PMID: 36806919; PMCID: PMC10909491.

  • An Automated Nanowell-Array Workflow for Quantitative Multiplexed Single-Cell Proteomics Sample Preparation at High Sensitivity

Ctortecka C, Hartlmayr D, Seth A, Mendjan S, Tourniaire G, Udeshi ND, Carr SA, Mechtler K. An Automated Nanowell-Array Workflow for Quantitative Multiplexed Single-Cell Proteomics Sample Preparation at High Sensitivity. Mol Cell Proteomics. 2023 Dec;22(12):100665.
DOI: https://doi.org/10.1016/j.mcpro.2023.100665. Epub 2023 Oct 14. PMID: 37839701; PMCID: PMC10684380.

  • Evidence of a role for CutRS and actinorhodin in the secretion stress response in Streptomyces coelicolor M145

McLean TC, Beaton ADM, Martins C, Saalbach G, Chandra G, Wilkinson B, Hutchings MI. Evidence of a role for CutRS and actinorhodin in the secretion stress response in Streptomyces coelicolor M145. Microbiology (Reading). 2023 Jul;169(7):001358. DOI: https://doi.org/10.1099/mic.0.001358.
PMID: 37418299; PMCID: PMC10433416.

  • Data-Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label-Free Single-Cell Proteomics

Truong, T., Webber, K. G. I., Madisyn Johnston, S., Boekweg, H., Lindgren, C. M., Liang, Y., Nydegger, A., Xie, X., Tsang, T.-M., Jayatunge, D. A. D. N., Andersen, J. L., Payne, S. H., Kelly, R. T., Angew. Chem. Int. Ed. 2023, e202303415.
DOI: https://doi.org/10.1002/anie.202303415

  • Robust and Easy-to-Use One-Pot Workflow for Label-Free Single-Cell Proteomics

Manuel Matzinger, Elisabeth Müller, Gerhard Dürnberger, Peter Pichler, and Karl Mechtler. Analytical Chemistry.
DOI: https://pubs.acs.org/doi/full/10.1021/acs.analchem.2c05022


2022

  • 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

  • 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.

  • 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 

  • 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.

  • 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. 

  • 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

  • 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

  • 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. 

  • 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. 

  • 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. 

2021

  • 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. 

  • 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.

  • Ultrasensitive NanoLC-MS of Subnanogram Protein Samples Using Second Generation Micropillar Array LC Technology with Orbitrap Exploris 480 and FAIMS PRO

Karel Stejskal, Jeff Opde Beeck, Gerhard Durnberger, et. al. Anal Chem. 2021 Jun. 29;93(25):8704-8710.
DOI: https://doi.org/10.1021/acs.analchem.1c00990.

  • Proteome Discoverer - A Community Enhanced Data Processing Suite for Protein Informatics

Benjamin C. Orsburn. Proteomes. 2021 Mar. 23;9(1):15. DOI: https://doi.org/10.3390/proteomes9010015.