JEOL Resources

JMS-S3000 SpiralTOF™ series Imaging Applications Notebook 2023

Mon, 13 Oct 2025 17:51:11 GMT

Edition August 2023

This is a compendium of mass spectrometry imaging applications notes and JEOL News articles based on the data acquired on JEOL ultra-high mass-resolution MALDI-TOFMS JMS-S3000 SpiralTOF™ series.

Introduction and Fundamentals　P1～

Mass Spectrometry Imaging using the JMS-S3000 "SpiralTOF™-plus" Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometer (Takaya Satoh, JEOL News, 55, 70-72, 2020)
Development of JMS-S3000: MALDI-TOF/TOF Utilizing a Spiral Ion Trajectory (Takaya Satoh, JEOL News, 45, 34-37, 2010)
High Mass Resolution MALDI-Imaging MS – High Stability of Peak Position during Imaging MS Measurement (MSTips No. 193)
The Relationship between Crystal Condition and Mass Resolving Power, Mass Accuracy (MSTips No.206)

Life Science / Biomolecules　P17〜

High mass-resolution MS imaging using JMS-S3000 "SpiralTOF™" and statistical data analysis (MSTips No. 370)
High Mass-Resolution MALDI-imaging MS for Drug Metabolism in Tissue Using the JMS-S3000 (MSTips No. 212)
High Mass Resolution MALDI-imaging MS Using JMS-S3000 SpiralTOF™ and msMicroImager (MSTips No. 211)
Fingerprint Analyses Using MALDI Imaging and SEM Imaging (MSTips No. 208)
MALDI-Imaging MS of Lipids on Mouse Brain Tissue Sections Using Negative Ion Mode (MSTips No. 196)

Polymers / Materials　P35〜

Degradation analysis of polyethylene terephthalate film by UV irradiation using imaging mass spectrometry and scanning electron microscopy (HS05)
Mass spectrometry imaging for degradation of polyethylene terephthalate by UV irradiation using JMS-S3000 "SpiralTOF™-plus" (MSTips No. 307)
A mass spectrometry imaging method for visualizing synthetic polymers combined with Kendrick mass defect analysis (MSTips No. 306)
A mass spectrometry imaging method for visualizing synthetic polymers by using average molecular weight and polydispersity as indices. (MSTips No. 305)
Mass spectrometry imaging on mixed conductive/non-conductive substrate using JMS-S3000 SpiralTOF™ (MSTips No. 288)
Analysis of organic compounds on an acrylic plate using JMS-S3000 "SpiralTOF™" (MSTips No. 251)
Ballpoint Ink Analyses Using LDI Imaging and SEM/EDS Techniques (MSTips No. 204)
Gunshot Residues (GSR) Analysis by Using MALDI Imaging
Analysis of Organic Thin Films by the Laser Desorption/Ionization Method Using the JMS-S3000 "SpiralTOF™" (Satoh, T., JEOL News, 49, 81-88, 2014)

MALDI-TOFMS imaging system JEOL×SCiLS

Thu, 10 Jun 2021 15:13:44 GMT

JMS-S3000 SpiralTOF™-plus MALDI-TOFMS imaging system

High mass-resolving power and high mass accuracy achieved by JEOL's unique SpiralTOF ion optics with 17 m flight path.
High mass-resolution can be achieved even for an imaging specimen with uneven surface.
Chemical noise in low m/z region is significantly reduced as PSD (post-source decay) ions are eliminated by the electric sectors used in the SpiralTOF ion optics.
Highly selective spatial distribution can be obtained by separating target analytes from interferences with high mass-resolution.

SCiLS™ – We turn data into knowledge!

SCiLS Lab MVS
Software for MS imaging data analysis

Data analysis based on the vendor-neutral imzML format
2D and 3D visualization allows a multitude of applications in pharmaceutical, medical, and industrial research
Advanced processing and analysis with next generation machine learning algorithms

▶ Comparative analysis
▶ Co-localization analysis
▶ Spatial segmentation
▶ Component analysis
▶ Classification model calculation
▶ On-tissue quantitation

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MALDI imaging brochure

Fri, 19 Mar 2021 13:04:15 GMT

Advanced statistical analysis of MALDI MS imaging data required by SpiralTOF-plus while taking full advantage of its high mass-resolving power.

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SpiralTOF Imaging Applications Notebook 2020

Thu, 11 Mar 2021 11:10:00 GMT

Applications concerning MALDI MS Imaging using the SpiralTOF.

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Degradation of PET by UV irradiation using S3000 - MSTips 307

Mon, 22 Jun 2020 12:04:46 GMT

Degradation analysis of PET film by UV irradiation using MALDI-MSI & FE-SEM-HS05

Mon, 22 Jun 2020 11:51:02 GMT

Degradation analysis of polyethylene terephthalate film by UV irradiation using imaging mass spectrometry and scanning electron microscopy

Product: JMS-S3000, JSM-7200F

Introduction

Surface analysis equipment is commonly used to evaluate industrial material for information such as elements, bonding states, and functional groups on the sample surface. However, commonly used tools like scanning electron microscopes (SEM) are not able to provide the elemental composition or structural information about the organic compounds present in/on the sample. Conversely, organic mass spectrometry (MS) can provide this information for organic molecules on surfaces and in the bulk material. Among the MS techniques available, matrix assisted laser desorption/ionization (MALDI) mass spectrometry is a powerful tool for the analysis of synthetic polymers. By using MALDI with a high-resolution time-of-flight mass spectrometer and Kendrick mass defect (KMD) analysis, polymer materials can be quickly analyzed to identify differences in monomer, polymer end groups, and their molecular weight distributions. More recently, MALDI mass spectrometry imaging (MALDI-MSI) has been used to visualize the locations of compounds on sample surfaces, thus suggesting that it is possible to obtain polymer molecular information present on sample surfaces, which is not possible by conventional surface analysis methods like SEM. In a previous report [1], we showed the effects of ultraviolet (UV) irradiation degradation for polyethylene terephthalate (PET) spots. In this report, we have expanded MALDI-MSI to analyzing a PET film that was exposed to UV radiation. Additionally, a SEM was used to look at the morphological differences in the PET film before and after UV irradiation.

Experimental

A 30 µm-thick PET film was used for the sample. First, the right-half of the PET film was masked with aluminum foil, and then UV irradiated for 30 minutes using Handicure 100 (manufactured by Mizuka Planning Co., Ltd.).

Figure 1. Schematic of the irradiation region of PET film using ultraviolet ray.

2,4,6-Trihydroxyacetophenone (THAP) was used as the matrix, and sodium trifluoroacetate (NaTFA) was used as the cationizing agent. THAP and NaTFA were dissolved in tetrahydrofuran (THF) at concentrations of 10 mg/mL and 1 mg/mL, respectively. A THAP and NaTFA mixture (10:1 v/v) solution was sprayed on the PET film with an airbrush.

The MALDI-MSI measurements were done by using the JMS-S3000 in SpiralTOF positive ion mode. The pixel size for the MSI images was 50 µm. The msMicroImager^TM software was used for MSI analysis, and msRepeatFinder was used for KMD analysis. A JSM-7200F field emission scanning electron microscope (FE- SEM), was used to look at the surface morphology using the conditions listed in Figure 2.

Results

Figure 2 shows the secondary electron images for the PET film surface before (A, B) and after (C, D) UV irradiation. These results were obtained by SEM without coating the sample for analysis. In particular, secondary electrons emitted from the sample surface are sensitive to irregularities which makes it suitable for looking at changes in sample surfaces. Figures 2A and B show the secondary electron images before UV irradiation (magnifications of 50,000 and 100,000, respectively), in which the PET surface is smooth. On the other hand, Figure 2C and D show the secondary electron images after UV irradiation (magnifications of 50,000 and 100,000, respectively), in which surface irregularities of approximately 100nm were observed. These results show that SEMs are effective for observing changes in morphology and nanostructures on sample surfaces.

Figure 2. Secondary electron image of PET film surface before (A,B) and after (C,D) ultraviolet irradiation.

FE-SEM conditions were Acceleration voltage: 0.8 kV, Signal：Secondary electron image, Pretreatment：without coating.

Figure 3A shows the averaged mass spectrum for the entire measurement area. Figure 3B shows the C₁₀H₈O₄ KMD plot for the average mass spectrum in which eight different PET series (192u intervals) were identified. Series I thru IV are exactly the same series observed previously in MSTips 307. These series were identified as sodium adduct ions for (I) cyclic oligomer, (II) COOH/COOH end groups, (III) cyclic oligomer + C₂H₄O, and (IV) COOH/OH end groups, respectively. Series I and III are components that were present before ultraviolet irradiation, and Series II and IV are the components that appear after ultraviolet irradiation. The Series I and II images (Figure 4A and 4B) were generated by summing the mass image intensities included in the KMD plot blue and red groups, respectively. The Series I ion intensities are relatively low in the irradiated side (left) so this means that UV irradiation reduces the presence of this series (Figure 4A). On the other hand, the Series II ion intensities are relatively high in the irradiated side (left) so this means that UV irradiation increases the presence of this series (Figure 4B). To show this degradation more clearly, Figure 4C normalizes Series II to Series I by ratioing their ion intensities (Series II/I) in each pixel. Figure 5 shows the Series II to VIII images using Series I for normalization (2×2 pixel binning). Figure 5 clearly shows that the Series III, V, and VIII, which have the same color tone for both the irradiated and unirradiated sections, are present in the sample regardless of UV irradiation. However, Series II, IV, VI, and VII show brighter color areas for the irradiated section of the sample, thus indicating that these PET series are generated by irradiating the surface with UV light.

Conclusions

In this report, we compared UV irradiated and non-irradiated PET thin films by using FE-SEM to observe morphology changes on the surface and MALDI-MSI to detect changes in molecular information on the film surface. Each technique provided complementary information about the UV degradation of a PET thin film.

References

[1] MSTips 307 “Mass spectrometry imaging for degradation of polyethylene terephthalate by UV irradiation using JMS-S3000 "SpiralTOF^TM-plus"”

Figure 3. (A) Averaged mass spectrum for the MSI measurement region and (B) KMD plot (base unit C₁₀H₈O₄, X=192). The KMD plot easily showed the presence of eight PET series (I) – (VIII).

Figure 4. Images of (A) the cyclic oligomer of PET series (Series I), (B) the ultraviolet degraded PET polymer series (Series II), and (C) Series II normalized to Series I.

Figure 5. The PET Series II –VIII images normalized with the Series I image.

MS imaging for visualizing synthetic polymers using average MW and p as indices - MSTips 305

Fri, 12 Jun 2020 11:19:28 GMT

Matrix assisted laser desorption/ionization (MALDI) mass spectrometry is a powerful tool for the analysis of synthetic polymers. This technique, when combined with a high-resolution time-of-flight mass spectrometer, can be used to identify differences in monomer, polymer end groups, and their molecular weight distributions. The molecular weight distribution is often expressed as number average molecular weight (M_n), weight average molecular weight (M_w), and dispersity (D). More recently, MALDI mass spectrometry imaging (MALDI-MSI) has been used to visualize the locations of compounds on sample surfaces. The MALDI-MSI raw data includes the position information (X and Y) as well as the mass spectral information (m/z and intensity) for each position. A target compound peak can then be specified to calculate the ion intensity for each pixel in order to draw a mass image. MALDI-MSI has been widely used to show the localization of proteins, peptides, lipids, and drugs on frozen tissue sections. However, this technique has not been widely used for polymer analysis. One reason for this is that polymers have molecular weight distributions which means that mass images based on specific degrees of polymerization (specific m/z value typically used by conventional methods) do not necessarily express a clear picture for the full polymer localization. In this report, we investigate a MSI visualization method for synthetic polymers that uses M_n,M_w and D as indices for visualization.

MS imaging for visualizing synthetic polymers combined with KMD - MSTips - 306

Fri, 12 Jun 2020 11:04:23 GMT

A mass spectrometry imaging method for visualizing synthetic polymers combined with Kendrick mass defect analysis

Product: JMS-S3000

Introduction

Matrix assisted laser desorption/ionization (MALDI) mass spectrometry is a powerful tool for the analysis of synthetic polymers. This technique, when combined with a high-resolution time-of-flight mass spectrometer, can be used to identify differences in monomer, polymer end groups, and their molecular weight distributions. The molecular weight distribution is often expressed as number average molecular weight (M_n), weight average molecular weight (M_w), and dispersity (D). More recently, MALDI mass spectrometry imaging (MALDI-MSI) has been used to visualize the locations of compounds on sample surfaces. However, this technique has not been widely used for polymer analysis. One reason for this is that polymers have molecular weight distributions which means that mass images based on specific degrees of polymerization (specific m/z value typically used by conventional methods) do not necessarily express a clear picture for the full polymer localization. In the previous MSTips 305 report [1], we proposed a new MALDI-MSI visualization method for synthetic polymers that used the M_n, M_w and D as indices. In this report, we have combined this method with the Kendrick Mass Defect (KMD) method to effectively visualize polymer series mixtures.

Experimental

A model sample was prepared using polyethylene glycol (PEG), polyethylene glycol monododecyl ether (PEG-C₁₂H₂₅), and polypropylene glycol (PPG) .The reagents used are shown in Table 1. A mixed solution of PEG, PEG-C₁₂H₂₅, α-CHCA, and NaTFA 1/0.1/10/1 (v/v/v/v) was spotted on the left-hand spot, and a mixed solution of PEG, PPG, α-CHCA, and NaTFA 1/0.1/10/1 (v/v/v/v) was spotted on the right-hand spot (Figure 1). The MALDI-MSI data was measured by using the SpiralTOF positive ion mode on the JMS-S3000. The pixel size was 50 μm, and the laser irradiation frequency was 50 times for each pixel. The MSI analysis and visualization was performed by using the JEOL msMicroImager™software, and the KMD analysis was performed by using the JEOL msRepeatFinder™ software.

Samples

Polyethylene glycol (PEG) M_w2000

Polyethylene glycol monododecyl ether (PEG-C₁₂H₂₅)

Polypropylene glycol (PPG) M_w 2000

1mg/mL (in MeOH)

Matrix

α-CHCA 10mg/mL (in MeOH)

Cationization

NaTFA 1mg/mL (in MeOH)

Table 1. Samples, matrix and cationization agent.

Fig. 1. Schematic of the model sample.

Results

The average mass spectrum for the entire sample region (right-hand and left-hand spots) is shown in Figure 2A. Two polymer distributions with repeat units of 44 u (C₂H₄O) were easily observed around m/z 900-1800 and m/z 1500-2800 that corresponded with PEG-C₁₂H₂₅ and PEG 2000, respectively. However, the polypropylene series with repeat units 58 u (C₃H₆O) was more difficult to observe in the average mass spectrum. The C₂H₄O KMD plot for the average mass spectrum is shown in Figure 2B. This plot clearly showed the presence of three polymer series as highlighted by the three colors (blue, red, and green). The two major series for PEG2000 (colored with blue) and PEG-C₁₂H₂₅ (colored with red), which both have C₂H₄O monomer units, made a horizontal line across the KMD plot. The minor series for PPG2000 (colored with green) showed a sloped line due to the fact that it has a repeat unit of C₃H₆O. These results clearly show the advantage of using a KMD plot to easily visualize polymer series, even with low intensity ions that can be difficult to observe in the mass spectrum. Using the KMD plot, three polymer peak lists were extracted from the average mass spectrum peak list and images for M_n and D were made for each polymer series. The PEG, PEG-C₁₂H₂₅ and PPG polymer peak lists contained 216, 84, and 70 peaks, respectively. It would be time consuming to use conventional methods that involve looking at all 370 mass images individually to make any reasonable determinations about the samples. However, the M_n and D were easily calculated using each extracted peak list. The corresponding M_n and D images for each polymer series are shown in Figure 3. From these images, the M_n values of PEG, PEG-C₁₂H₂₅ and PPG were approximately 2200, 1350 and 2200, respectively, and the D values of PEG, PEG-C₁₂H₂₅ and PPG were approximately 1.01, 1.015 and 1.008, respectively.

Fig. 2. (A) Averaged mass spectrum showing two clearly defined polymer series with a repeat unit of 44 u (C₂H₄O). (B) KMD plot (based on C₂H₄O) for the entire peak list from the averaged mass spectrum. The PEG and PEG-C₁₂H₂₅ polymer series were observed as horizontal lines across the plot. Also, the PPG series that was difficult to find in the mass spectrum is clearly observed in the KMD plot.

Fig. 3. The M_nand D images for PEG, PEG-C₁₂H₂₅ and PPG polymer series.

Conclusions

In this report, we have introduced the advantages of combining KMD analysis with the visualizing method reported in MSTips 305 to analyze samples containing multiple synthetic polymer series. By using the KMD method, it is easy to visualize each polymer series, even for minor components that are difficult to identify in the mass spectrum.

References

[1]MSTips 305 A mass spectrometry imaging method for visualizing synthetic polymers by using average molecular weight and polydispersity as indices.

Tissue imaging with high mass-resolving power and high-energy CID

Thu, 05 Mar 2020 17:46:18 GMT

High resolution mass spectrometry imaging

In MALDI imaging mass spectrometry, the sample is moved beneath the focused laser beam to create a time-dependent series of mass spectra where each time corresponds to a specific spatial location. Analysis of the data allows the researcher to visualize the spatial distribution of specific compounds on the sample surface. Because the SpiralTOF’s 17-meter flight path minimizes the effect of topographic variations on the sample surface, high mass-resolving power can be maintained for tissue imaging.

Mass Spectrometry Imaging (MSI) on mixed conductive/non-conductive substrate using JMS-S3000 SpiralTOF™ - MSTips - 288

Thu, 05 Mar 2020 17:43:07 GMT

Experimental

To create a model substrate, we formed conductive and non-conductive parts using metal patterns (Au 100 nm/Cr 30 nm) on a 1-mm-thick quartz glass substrate, alternating conductive with non-conductive parts at intervals of 400 μm. We used a red permanent marker to ionize the main component without applying a matrix compound. The letters "MS" were written with this marker so that they straddled the conductive and non-conductive parts on the model substrate. We then fixed the model substrate and the stainless-steel target plate with conductive tape (Fig. 2). Mass spectrometry imaging was performed without gold deposition. Thereafter, we used gold deposition on the same sample and performed mass spectrometry imaging again. All mass spectrometry imaging were performed in SpiralTOF positive-ion mode. Pixel size was 50 μm; number of laser shots was 50 per pixel.

JEOL Resources

JMS-S3000 SpiralTOF™ series Imaging Applications Notebook 2023

Table of Contents

Introduction and Fundamentals P1～

Life Science / Biomolecules P17〜

Polymers / Materials P35〜

MALDI-TOFMS imaging system JEOL×SCiLS

JMS-S3000 SpiralTOF™-plus MALDI-TOFMS imaging system

SCiLS™ – We turn data into knowledge!

SCiLS Lab MVS Software for MS imaging data analysis

Click to Download the Full Brochure Below

MALDI imaging brochure

Click Below To View The Brochure.

SpiralTOF Imaging Applications Notebook 2020

Please click below to Download

Degradation of PET by UV irradiation using S3000 - MSTips 307

Degradation analysis of PET film by UV irradiation using MALDI-MSI & FE-SEM-HS05

Degradation analysis of polyethylene terephthalate film by UV irradiation using imaging mass spectrometry and scanning electron microscopy

Introduction

Experimental

Results

Conclusions

References

MS imaging for visualizing synthetic polymers using average MW and p as indices - MSTips 305

MS imaging for visualizing synthetic polymers combined with KMD - MSTips - 306

A mass spectrometry imaging method for visualizing synthetic polymers combined with Kendrick mass defect analysis

Introduction

Experimental

Results

Conclusions

References

Tissue imaging with high mass-resolving power and high-energy CID

High resolution mass spectrometry imaging

Mass Spectrometry Imaging (MSI) on mixed conductive/non-conductive substrate using JMS-S3000 SpiralTOF™ - MSTips - 288

Experimental

Introduction and Fundamentals　P1～

Life Science / Biomolecules　P17〜

Polymers / Materials　P35〜

SCiLS Lab MVS
Software for MS imaging data analysis