Dataset DOI: 10.5061/dryad.kkwh70shx

This dataset contains mass spectrometry imaging datasets derived from the imaging of kidney samples and from prepared solutions from bovine fetuin. For the image analysis, the necessary imzML, ibh, and ibd files are provided. Load this data into image viewing software such as MSiReader. For the solution analysis, the raw data can be uploaded to an image viewing software or the raw files can be viewed directly in Freestyle.  

In this work, we utilize doped electrospray with 350 uM ammonium fluoride and an electrospray diverter to investigate their impact on glycan signal. This used 4 tissues and 3 solution samples. The abundance of observed glycans between the two conditions were compared to evaluate a signal enhancement factor.  

Description of the data and file structure

Data was generated by imaging prepared N-glycans by IR-MALDESI. The ESI solvent consisted of 50% ACN, 1 mM acetic acid, and 350 uM ammonium fluoride. An electrospray diverter was also used to reduce background signals. Tissue halves were directly compared between the use of the ESI doping and diverter vs control condition. Therefore, each tissue is divided into a half with diverting and doping, and a control half, shown in the data files. 

Files and variables

imzML files are universal imaging files that can be opened by many software. ibh and ibd files are often required to open imzML files and are included as well. 

File names are labeled to explain their contents. The word bottom or top in the file name refers to the half of the tissue that was analyzed - either the bottom or the top. The half used for control or experimental was randomized. The word control_nodiverter or NH4F_diverter indicates the condition tested. Control_nodiverter refers to the standard process of performing IR-MALDESI imaging, while the NH4F_diverter refers to using both of those techniques to enhance signal. And the number refers to the sample number used. Many sample numbers are skipped as those samples failed at some point during the data collection and were not used in analysis. 

File: Glycan4_bottom_control_nodiverter.imzML

Description: imzML file for glycan4 sample control condition. Image of human kidney sample sectioned at 3 um. Sample was imaged at 150 um x 150 um spot size and step size. This tissue half was from the bottom of the kidney sample and used a control ESI solvent consisting of 50% ACN, 1 mM acetic acid. The ESI diverter was not used and the ion injection time was set at 90 ms to collect this data. 

File: Glycan4_bottom_control_nodiverter.ibd

Description:  ibd file for glycan4 sample experimental condition

File: Glycan4_bottom_control_nodiverter.ibh

Description: ibh file for glycan4 sample control condition

File: Glycan4_top_NH4F_diverter.imzML

Description: imzML file for glycan4 sample experimental condition. Image of human kidney sample sectioned at 3 um. Sample was imaged at 150 um x 150 um spot size and step size. This tissue half was from the top of the kidney sample and used a doped ESI solvent consisting of 50% ACN, 1 mM acetic acid, 350 uM NH4F. The ESI diverter was used and set to turn on 15 ms after the laser was fired. While the ion injection time was set at 90 ms to collect this data, ions were only able to enter the mass spectrometer for the first 15 ms. 

File: Glycan4_top_NH4F_diverter.ibd

Description: ibd file for glycan4 sample experimental condition

File: Glycan4_top_NH4F_diverter.ibh

Description: ibh file for glycan4 sample control condition. 

File: Glycan7_bottom_control_nodiverter.imzML

Description: imzML file for glycan7 sample control condition. Replicate 2 for the control tissue imaging. This tissue has the same parameters for generation and data collection as the first replicate. 

File: Glycan7_bottom_control_nodiverter.ibd

Description: ibd file for glycan7 sample control condition

File: Glycan7_bottom_control_nodiverter.ibh

Description:  ibh file for glycan7 sample control condition

File: Glycan7_top_NH4F_diverter.imzML

Description: imzML file for glycan7 sample experimental condition. Replicate 2 for the control tissue imaging. This tissue has the same parameters for generation and data collection as the first replicate. 

File: Glycan7_top_NH4F_diverter.ibd

Description:  ibh file for glycan7 sample control condition

File: Glycan7_top_NH4F_diverter.ibh

Description: ibh file for glycan7 sample experimental condition

File: Glycan9_bottom_NH4F_diverter.imzML

Description: imzML file for glycan9 sample experimental condition. Replicate 3 for the control tissue imaging. This tissue has the same parameters for generation and data collection as the first replicate. 

File: Glycan9_bottom_NH4F_diverter.ibd

Description:  ibd file for glycan4 sample experimental condition

File: Glycan9_bottom_NH4F_diverter.ibh

Description: ibh file for glycan9 sample experimental condition

File: Glycan9_top_control_nodiverter.imzML

Description: imzML file for glycan9 sample control condition. Replicate 3 for the control tissue imaging. This tissue has the same parameters for generation and data collection as the first replicate. 

File: Glycan9_top_control_nodiverter.ibd

Description: ibd file for glycan9 sample control condition

File: Glycan9_top_control_nodiverter.ibh

Description: ibh file for glycan9 sample control condition

File: Glycan10_bottom_control_nodiverter.imzML

Description: imzML file for glycan10 sample control condition. Replicate 4 for the control tissue imaging. This tissue has the same parameters for generation and data collection as the first replicate. 

File: Glycan10_bottom_control_nodiverter.ibd

Description: ibd file for glycan10 sample control condition

File: Glycan10_bottom_control_nodiverter.ibh

Description: ibh file for glycan10 sample control condition

File: Glycan10_top_NH4F_diverter.imzML

Description: imzML file for glycan10 sample experimental condition. Replicate 4 for the control tissue imaging. This tissue has the same parameters for generation and data collection as the first replicate. 

File: Glycan10_top_NH4F_diverter.ibd

Description: ibd file for glycan10 sample experimental condition

File: Glycan10_top_NH4F_diverter.ibh

Description: ibh file for glycan10 sample experimental condition

File: bovine_fetuin_control_nodiverter_1.raw, bovine_fetuin_control_nodiverter_2.raw, bovine_fetuin_control_nodiverter_3.raw

Description: raw files of signals generated analyzing a solution of bovine fetuin in the control condition. These aqueous samples were prepared from the glycoprotein bovine fetuin to generate a solution of cleaved N-glycans. 5 uL of solution were pipetted onto a hydrophobic slide and placed directly below the laser to ablate the solution. 25 laser shots were used for each replicate. In these replicates, the ESI solution consisted of 50% ACN, 1 mM acetic acid and the ESI diverter was not used. 

File: bovine_fetuin_NH4F_diverter_1.raw, bovine_fetuin_NH4F_diverter_2.raw, bovine_fetuin_NH4F_diverter_3.raw

Description: raw file of signals generated analyzing a solution of bovine fetuin in the experimental condition. These aqueous samples were prepared from the glycoprotein bovine fetuin to generate a solution of cleaved N-glycans. 5 uL of solution were pipetted onto a hydrophobic slide and placed directly below the laser to ablate the solution. 25 laser shots were used for each replicate. In these replicates, the ESI solution consisted of 50% ACN, 1 mM acetic acid, and 350 uM NH4F and the ESI diverter was used, set to turn on 15 ms after the laser was fired. 

Code/software

Many software options are available to open imzML files. The one used for the analysis of this study is MSiReader v3.08. Raw files were opened with Freestyle 1.8 SP 2.