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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

Rapid Commun Mass Spectrom. 2021 May. ;e9128.. doi: https://doi.org/10.1002/rcm.9128. Daniel P. Zolg, Siegfried Gessulat, Carmen Paschke, et. al.


RECENT PUBLICATIONS FEATURING MSAID SOFTWARE

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

  • 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

J. Proteome Res. 2022, 21, 10, 2453–2461. doi: https://doi.org/10.1021/acs.jproteome.2c00337. Kendall R. Johnson, Michal Greguš, and Alexander R. Ivanov.

  • Deep Single-Shot NanoLC-MS Proteome Profiling with a 1500 Bar UHPLC System, Long Fully Porous Columns, and HRAM MS

J. Proteome Res. 2022 Sept. doi: https://doi.org/10.1021/acs.jproteome.2c00270. Runsheng Z., Karel S., Christopher Pynn, et al.

  • 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

 J. Proteome Res. 2022 Aug. doi: https://doi.org/10.1021/acs.jproteome.2c00409. Andikan J. Nwosu, Santosh A. Misal, Thy Truong, et al.

  • Protein SUMOylation is a sex-specific regulator of fear memory formation in the amygdala

2022 Jul. doi: https://doi.org/10.1016/j.bbr.2022.113928. Aspen Gustin, Shaghayegh Navabpour, KaylaFarrella, et al.

  • Label-Free Profiling of up to 200 Single-Cell Proteomes per Day Using a Dual-Column Nanoflow Liquid Chromatography Platform

Anal. Chem. 2022 Apr. 94, 15, 6017–6025. doi: https://doi.org/10.1021/acs.analchem.2c00646. Kei G. I. Webber, Thy Truong, S. Madisyn Johnston, et al.

  • Capillary Electrophoresis Coupled to Electrospray Ionization Tandem Mass Spectrometry for Ultra-Sensitive Proteomic Analysis of Limited Samples

Anal. Chem. 2022, 94, 2, 704–713. Jan 2022. doi: https://doi.org/10.1021/acs.analchem.1c02929. Kendall R. Johnson, Michal Greguš, James C. Kostas, and Alexander R. Ivanov

  • Proteomic Analysis Reveals Sex-Specific Protein Degradation Targets in the Amygdala During Fear Memory Formation

Front. Mol. Neurosci. 2021 Sept. 14:716284. doi: https://doi.org/10.3389/fnmol.2021.716284. Farrell K, Musaus M, Navabpour S, et al.

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

Anal Chem. 2021 Jun. 29;93(25):8704-8710. doi: https://doi.org/10.1021/acs.analchem.1c00990. Karel Stejskal, Jeff Opde Beeck, Gerhard Durnberger, et. al.
  • Proteome Discoverer - A Community Enhanced Data Processing Suite for Protein Informatics

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