JEOL Resources

Structural analysis of polyethylene terephthalates with different crystallinity using JMS-S3000 "SpiralTOF™-plus 2.0"

Thu, 27 Aug 2026 16:18:20 GMT

MSTips No. 407

Poly (ethylene terephthalate) (PET) is a thermoplastic polyester obtained by polycondensation of ethylene glycol and terephthalic acid, and has excellent properties such as transparency, toughness, rigidity, and heat resistance (Figure 1). PET can be roughly divided into two types depending on processability: crystalline PET (C-PET) and amorphous PET (A-PET). C-PET has a high density due to the regular arrangement of the molecules in the crystallized part, and is characterized by high strength and heat resistance. A-PET is characterized by high impact strength and easy bending. However, due to long-term use or exposure to heat, the amorphous portion of A-PET slowly crystallizes, causing internal stress due to changes in density and breaking the polymer chains, resulting in poor flexibility, impact resistance, and strength. Therefore, a polymer was devised in which about 30-40% of the ethylene glycol in PET was replaced with cyclohexanedimethanol; this polymer is called glycol-modified PET (G-PET, PETG) (Figure 2). G-PET is treated as an amorphous resin because the polymer does not crystallize during molding. In a previous report [1], we performed structural analysis of two types of commercially available PET resins (PET film and PET plate) using reactive pyrolysis GC-TOFMS and NMR, and confirmed that the PET film was PET and the PET plate was G-PET. In this report, we analyzed the oligomer region of the same samples using a high-resolution MALDI-TOFMS JMS-S3000 "SpiralTOF™-plus 2.0" in combination with Kendrick Mass Defect (KMD) analysis.

End group analysis of poly(methyl methacrylate) using MALDI-TOFMS and GC-TOFMS

Thu, 27 Aug 2026 16:13:55 GMT

MSTips No. 404

Mass spectrometry can be used to analyze synthetic polymers, providing a variety of information, such as the main chain structure, end group structure, and molecular weight distribution (average molecular weight, polydispersity). Analysis of end group structure is particularly important for the following reasons.

The physical properties of polymer materials can change depending on the end groups, even though they are relatively small part of the whole polymer molecules.
End group structure might change (or degrade) due to environmental exposures.
End group structure can provide insight into the polymerization mechanism.

MALDI is a soft ionization method that allows the observation of polymer molecules as singly charged ions. Using high-resolution MALDI-TOFMS, it is possible to elucidate the elemental compositions of end groups from the accurate masses. On the other hand, pyrolysis GC-TOFMS analyzes the pyrolysis products produced by instantaneous heating of a polymer. Mainly monomers and dimers are observed, but if pyrolysis products containing end groups are observed, structural information on the end groups can be obtained. In this report, we performed structural analysis of the end groups of poly(methyl methacrylate) by using MALDI-TOFMS and pyrolysis GC-TOFMS in a complementary manner.

Analysis of mPEG5K-Phosphate using JMS-S3000 "SpiralTOF™-plus 2.0"

Thu, 27 Aug 2026 16:09:12 GMT

MSTips No. 402

The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is a powerful tool for polymer analysis. Since MALDI generates mainly singly-charged ions, m/z values from the mass spectrum are the same as the polymer ion's mass. In general, polymer analysis by MALDI-TOFMS is performed in positive ion mode because the sample solution is added to the matrix and cationizing agent solution. On the other hand, a polymer including sulfate or phosphate groups at the end group can be measured in the negative ion mode. In MSTips No. 333, we reported the measurement results of anionic surfactants less than m/z 1000. In this application note, we report the measurement of polyethylene glycol (average molecular weight 5000) having phosphate groups as an end group.

Composition analysis of EO-PO copolymers using JMS-S3000 “SpiralTOF™-plus2.0” and “msRepeatFinder V6”

Thu, 27 Aug 2026 16:02:26 GMT

MSTips No. 399

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOFMS) is a powerful tool for polymer analysis. Since MALDI mainly produces singly charged ions, the m/z values in the mass spectrum is the masses of the polymer ions. By using high mass-resolution MALDI-TOFMS, it is possible to easily distinguish polymer series based on differences in repeating units and end group composition, and to calculate the molecular weight distribution of each series. Recently, the Kendrick Mass Defect (KMD) method has made it possible to easily visualize polymer series contained in complex high mass-resolution mass spectra. When the molecular weight of a sample is several thousand or more, it is known that electrospray ionization (ESI), a typical soft ionization method along with MALDI, tends to produce mainly multiply charged ions, making it difficult to directly analyze the mass spectrum, let alone perform KMD analysis. Therefore, the combination of the high mass-accuracy of the JMS-S3000 “SpiralTOF™-plus2.0” and KMD analysis is particularly effective for the analysis of copolymers. Here, we will report on the binary copolymer search function newly added to msRepeatFinder V6 and the resulting compositional analysis of EO-PO copolymers using the degree of polymerization plot.

High mass-resolution MS imaging using JMS-S3000 "SpiralTOF™" and statistical data analysis

Tue, 25 Aug 2026 08:37:00 GMT

MSTips No. 370

Imaging mass spectrometry (MSI) using matrix-assisted laser desorption/ionization (MALDI) is a technique for visualizing the distribution of organic compounds on a sample surface. Applications are being expanded mainly for proteins, peptides, lipids, drugs, and their metabolites on the surface of frozen tissue sections. MALDI-MSI scans the laser irradiation position two-dimensionally on the sample surface and acquires a mass spectrum at each laser irradiation position. By analyzing this series of mass spectra with two-dimensional positional information, the distribution of organic compounds with arbitrary molecular weights on the sample surface can be drawn as an extracted mass image.

The JMS-S3000 SpiralTOF™ is a time-of-flight mass spectrometer (TOFMS) with patented spiral trajectory ion optics. Because it has a flight distance of 17 m, which is longer than ordinary reflectron TOFMS, high mass resolution can be achieved even in MSI, where the surface condition of the sample is often uneven. In addition, the ion optical system is composed of sector electric fields, which makes it possible to remove post-source decay (PSD) ions, and it is also possible to detect trace components near the baseline with high mass resolution. Therefore, even in MALDI-MSI, it is possible to separate compounds with the same nominal mass but different exact masses (isobars) and draw a clear distribution of the compounds. In this report, we report the statistical analysis of high-mass resolution MALDI-MSI data of various lipids in biological samples.

Structural analysis of a small molecule using JMS-S3000 "SpiralTOF™-plus 2.0" ー MS/MS measurement of a photodegradation product of reserpine

Tue, 25 Aug 2026 08:33:52 GMT

MSTips No. 365

High mass-resolution MALDI-TOFMS can determine the elemental compositions of target compounds from their measured accurate masses. MS/MS measurement is effective in elucidating the chemical structure, which is difficult to infer from accurate mass information. MS/MS measurement using JMS-S3000 "SpiralTOF™-plus 2.0" with a TOF-TOF option can detect fragment ions generated by high-energy collision-induced dissociation(HE-CID). HE-CID is a technique of fragmenting precursor ions by a single collision. It is known to provide more structural information than low-energy collision-induced dissociation, which fragments precursor ions by multiple collisions. On the other hand, since MALDI-TOFMS is difficult to connect online with pre-separation methods such as liquid chromatography, the target compounds must be separated by only their masses. High precursor ion selectivity is required to obtain accurate structural information for components that are close in their masses. SpiralTOF™-plus 2.0 with TOF-TOF option can achieve high precursor ion selectivity due to the long flight path of the spiral ion optics used in the 1^st TOFMS. In this application note, we report the structural elucidation of a photodegradation product of reserpine as an example of structural analysis of a component close to a possible interference in mass by MS/MS measurement using the SpiralTOF™-plus 2.0 with TOF-TOF option.

Analysis of oligonucleotides using JMS-S3000 "SpiralTOF™-plus 2.0"

Tue, 25 Aug 2026 08:31:04 GMT

MSTips No. 364

A nucleotide is a compound in which a phosphate group is bound to a nucleoside consisting of a base and a sugar and is a building block of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acid drugs are attracting attention as therapeutic agents for diseases that have been difficult to treat, and as of October 2022, 16 nucleic acid drugs have been approved in Japan, U.S.A., or EU¹). In recent years, synthesized oligonucleotides have been utilized as nucleic acid medicines. Molecular weight confirmation of synthesized oligonucleotides is important for the quality control of pharmaceuticals. In this report, we used the synthesized oligonucleotide (Table 1) as a sample and measured it with a MALDI-TOFMS.

Elemental Composition Determination of Polymer End Groups Using Accurate Mass

Tue, 25 Aug 2026 08:24:05 GMT

MSTips No. 357

A molecular weight of a polymer species can be confirmed by combining soft ionization methods such as matrix-assisted laser desorption/ionization (MALDI) field desorption (FD), electrospray ionization (ESI), and a high resolution mass spectrometer capable of accurate mass measurements, such as a time-of-flight mass spectrometer (TOFMS). From the obtained mass spectrum, it is possible to identify polymer species (monomer identification), identify differences in end groups, and calculate the molecular weight distribution of each polymer series. Recently, it has been possible to efficiently overview the information in the mass spectra of complex polymer mixtures using a Kendrick Mass Defect (KMD) analysis software, msRepeatFinder. Determining the elemental composition of the end groups of the polymer series identified in this way is essential for confirming the state of polymer synthesis reactions, quality control of products, and analysis of degradation mechanisms. In this report, we introduce the procedure for determining the elemental compositions of the end groups from the accurate mass information of the polymer.

Structural analysis of anionic surfactants in MALDI negative ion mode using "SpiralTOF™-plus"

Wed, 05 Aug 2026 11:47:59 GMT

MSTips No. 333

The matrix-assisted laser desorption ionization time-of-flight mass spectrometer (MALDI-TOFMS) is a powerful tool in analyzing polymers. Since MALDI mainly produces singly charged ions, m/z values in the mass spectrum are the same as polymer ions' mass. Using the high mass resolution MALDI-TOFMS, it is possible to identify the compositions of polymer series by their repeating unit and the end-group, and calculate the molecular weight distributions of each. The Kendrick Mass Defect (KMD) was recently applied to the polymer analysis to visualize polymer series contained in complex high-mass resolution mass spectra. In addition, the TOF-TOF option enables structural analysis, especially for end-group analysis, of polymers from fragment ions generated by high-energy collision-induced dissociation (HE-CID). In polymer analysis with MALDI-TOFMS, sample, matrix and cationizing agent solution are mixed, dropped onto a target plate, air-dried, and measured. In general, the target polymer ions will be observed in the positive ion mode as [M+Li]⁺, [M+Na]⁺ or [M+K]⁺ according to the cationizing agents. However, polymers that have sulfate or phosphate end-groups can be detected in the negative ions. In this report, we will show the analysis of the mixture of anionic and nonionic surfactants.

Analysis of degraded polystyrene by UV irradiation using high-resolution MALDI-TOFMS and pyrolysis-GC-QMS

Thu, 30 Jul 2026 18:51:47 GMT

MSTips No. 322

Polymers can be degraded by the effects of light, oxygen, heat, etc. so it is important to understand how the polymer structures change during degradation. Pyrolysis gas chromatograph quadrupole mass spectrometer (Py-GC-QMS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOFMS) are powerful tools for analyzing polymeric materials. Py-GC-QMS is a method that instantaneously heats a sample with a pyrolyzer and then analyzes the pyrolysis products by GC-MS. Since most of the pyrolysis products are related to monomers and dimers, this technique allows for easy identification of the polymer substructures which is useful for identifying changes to the polymer when degradation occurs. MALDI-TOFMS involves a soft ionization technique that can directly ionize and analyze the intact polymer molecules and often produces singly-charged ions even for high molecular weight compounds. As a result, the m/z axis of the mass spectrum is equal to the mass of the ions, thus making it easy to interpret polymer distributions. Additionally, when MALDI is used with a high-resolution TOFMS, the accurate mass of each ion in the polymer series can be used to calculate their elemental compositions. Moreover, the molecular weight distribution of polymers can be calculated from the ion intensity distribution. In this work, we used Py-GC-QMS and high-resolution MALDI-TOFMS to evaluate the effects of UV irradiation on polystyrene (PS).