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Publications

 

How to cite MSAID Software

The following publications by the MSAID team describe the technology in more detail:

  • 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 Publication featuring MSAID Software

Here is a compilation of publications from scientists and colleagues who use INFERYS, INFERYS Rescoring, or CHIMERYS technologies for their research.

  • 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
  • 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
  • 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

  • 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

  • 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.