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(1) Robichaud, G.; Garrard, K. P.; Barry, J. A.; Muddiman, D. C. MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform. J. Am. Soc. Mass Spectrom. 2013, 24 (5), 718–721.

(2) Bokhart, M. T.; Nazari, M.; Garrard, K. P.; Muddiman, D. C. MSiReader v1. 0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses. J. Am. Soc. Mass Spectrom. 2017, 29 (1), 8–16.

(3) Nuñez, J. R.; Anderton, C. R.; Renslow, R. S. Optimizing Colormaps with Consideration for Color Vision Deficiency to Enable Accurate Interpretation of Scientific Data. PLOS ONE 2018, 13 (7), e0199239. https://doi.org/10.1371/journal.pone.0199239.

(4) Knizner, K. T.; Kibbe, R. R.; Garrard, K. P.; Nuñez, J. R.; Anderton, C. R.; Muddiman, D. C. On the Importance of Color in Mass Spectrometry Imaging. J. Mass Spectrom. 2022, 57 (12). https://doi.org/10.1002/jms.4898.

(5) Pedrioli, P. MSConvert Tool from Proteowizard. http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML.

(6) Pedrioli, P. G. A.; Eng, J. K.; Hubley, R.; Vogelzang, M.; Deutsch, E. W.; Raught, B.; Pratt, B.; Nilsson, E.; Angeletti, R. H.; Apweiler, R.; Cheung, K.; Costello, C. E.; Hermjakob, H.; Huang, S.; Julian, R. K.; Kapp, E.; McComb, M. E.; Oliver, S. G.; Omenn, G.; Paton, N. W.; Simpson, R.; Smith, R.; Taylor, C. F.; Zhu, W.; Aebersold, R. A Common Open Representation of Mass Spectrometry Data and Its Application to Proteomics Research. Nat. Biotechnol. 2004, 22 (11), 1459–1466. https://doi.org/10.1038/nbt1031.

(7) Kibbe, R. R.; Muddiman, D. C. Achieving Sub-Parts-per-Million Mass Measurement Accuracy on an Orbitrap Mass Spectrometry Imaging Platform without Automatic Gain Control. J. Am. Soc. Mass Spectrom. 2023, jasms.3c00004. https://doi.org/10.1021/jasms.3c00004.

(8) Schramm, T.; Hester, Z.; Klinkert, I.; Both, J.-P.; Heeren, R. M. A.; Brunelle, A.; Laprévote, O.; Desbenoit, N.; Robbe, M.-F.; Stoeckli, M.; Spengler, B.; Römpp, A. ImzML--a Common Data Format for the Flexible Exchange and Processing of Mass Spectrometry Imaging Data. J. Proteomics 2012, 75 (16), 5106–5110. https://doi.org/10.1016/j.jprot.2012.07.026.

(9) imzML / imzML Validator · GitLab. GitLab. https://gitlab.com/imzML/imzMLValidator (accessed 2022-09-09).

(10) Race, A. M.; Römpp, A. Error-Free Data Visualization and Processing through ImzML and MzML Validation. Anal. Chem. 2018, 90 (22), 13378–13384. https://doi.org/10.1021/acs.analchem.8b03059.

(11) METASPACE annotation platform. https://metaspace2020.eu/ (accessed 2022-09-09).

(12) Pace, C. L.; Garrard, K. P.; Muddiman, D. C. Sequential Paired Covariance for Improved Visualization of Mass Spectrometry Imaging Datasets. J. Mass Spectrom. 2022, 57 (7). https://doi.org/10.1002/jms.4872.

(13) Muddiman, D. C.; Rockwood, A. L.; Gao, Quanyin.; Severs, J. C.; Udseth, H. R.; Smith, R. D.; Proctor, Andrew. Application of Sequential Paired Covariance to Capillary Electrophoresis Electrospray Ionization Time-of-Flight Mass Spectrometry: Unraveling the Signal from the Noise in the Electropherogram. Anal. Chem. 1995, 67 (23), 4371–4375. https://doi.org/10.1021/ac00119a027.

(14) Muddiman, D. C.; Huang, B. M.; Anderson, G. A.; Rockwood, A.; Hofstadler, S. A.; Weir-Lipton, M. S.; Proctor, A.; Wu, Q.; Smith, R. D. Application of Sequential Paired Covariance to Liquid Chromatography-Mass Spectrometry Data Enhancements in Both the Signal-to-Noise Ratio and the Resolution of Analyte Peaks in the Chromatogram. J. Chromatogr. A 1997, 771 (1–2), 1–7. https://doi.org/10.1016/S0021-9673(97)00069-1.

(15) Eisenberg, S. M.; Knizner, K. T.; Muddiman, D. C. Development of an Object-Based Image Analysis Tool for Mass Spectrometry Imaging Ion Classification. Anal. Bioanal. Chem. 2023. https://doi.org/10.1007/s00216-023-04764-x.

(16) Khodjaniyazova, S.; Nazari, M.; Garrard, K. P.; Matos, M. P. V.; Jackson, G. P.; Muddiman, D. C. Characterization of the Spectral Accuracy of an Orbitrap Mass Analyzer Using Isotope Ratio Mass Spectrometry. Anal. Chem. 2018, 90 (3), 1897–1906. https://doi.org/10.1021/acs.analchem.7b03983.

(17) Rockwood, A. L. Relationship of Fourier Transforms to Isotope Distribution Calculations. Rapid Commun. Mass Spectrom. 1995, 9 (1), 103–105. https://doi.org/10.1002/rcm.1290090122.

(18) Wang, Z.; Bovik, A.; Sheikh, H.; Simoncelli, E. Image Quality Assessment: From Error Visibility to Structural Similarity. Image Process. IEEE Trans. On 2004, 13, 600–612. https://doi.org/10.1109/TIP.2003.819861.

(19) Ekelöf, M.; Garrard, K. P.; Judd, R.; Rosen, E. P.; Xie, D.-Y.; Kashuba, A. D. M.; Muddiman, D. C. Evaluation of Digital Image Recognition Methods for Mass Spectrometry Imaging Data Analysis. J. Am. Soc. Mass Spectrom. 2018, 29 (12), 2467–2470. https://doi.org/10.1007/s13361-018-2073-0.

(20) Verdun, F. R.; Ricca, T. L.; Marshall, A. G. Beating the Nyquist Limit by Means of Interleaved Alternated Delay Sampling: Extension of Lower Mass Limit in Direct-Mode Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Appl. Spectrosc. 1988, 42 (2), 199–203.

(21) Giancaspro, C.; Comisarow, M. B. Exact Interpolation of Fourier Transform Spectra. Appl. Spectrosc. 1983, 37 (2), 153–166. https://doi.org/10.1366/0003702834633984.