Division for Mass Spectrometry
The Mass Spectrometry Laboratory supports various analyses ranging from Proteomics to Metabolomics using mass spectrometers, and services are provided as consignment analysis or joint research.
To use the consignment analysis services or to conduct joint research with us, first send an email with your inquiry to our laboratory address. We will hold individual discussions. Then we will ask you to submit the consignment analysis request form or joint research application form（→Click here for the form）。
* We are providing some services to non-university users from April 2018.
* When using our laboratory, refer to the usage method for the entire center（→Click here） including the Mass Spectrometry Laboratory, and then submit the user registration. Registration is necessary every year.
Mass spectrometer installed in our laboratory
The following 4 systems are in continuous operation at our laboratory, and are used according to the type and purpose of analysis.
1. Quadrupole-Time of flight [Q-Tof] mass spectrometer
Triple TOF 5600 + system (SCIEX)
2. Quadrupole-Time of flight [Q-Tof] mass spectrometer
Xevo-G2-S system (Waters)
3. Tandem/triple quadrupole [QqQ] mass spectrometer
LC-MS 8030 Plus System (Shimadzu Corporation)
4. Matrix-assisted laser dissociation/ionization-Time of flight [MALDI-Tof] mass spectrometer
Ultraflex (Bruker)
* Liquid Chromatography [LC] or Supercritical Fluid Chromatography [SFC] are used as the preliminary separation equipment for 1 to 3.
Analyses that can be performed at our laboratory.
The following analyses can be performed at our laboratory.
We can support various other analyses, contact us when you want to conduct analyses that are not on the list.
Identification of proteins and peptides
Modification analysis of proteins and peptides
Quantitative proteome analysis
Precision mass measurement of proteins and peptides
Quantification of compounds and metabolites
Precision mass measurement of compounds
Structural estimation and structural comparison of compounds
Comprehensive measurement of compounds and metabolites
Quantitative metabolome analysis
Fractionation of proteins and peptides (Isoelectric point, and molecular weight)
Support for searching various biomarkers
Consignment analysis
Summary of each analysis
■ Protein identification analysis using SCIEX Triple TOF5600+
Processes from gel digestion of the samples under custody to measurements using mass spectrometers, database searches, and identification of proteins are implemented by staff members.
Samples are measured with the Quadrupole-Time of flight [Q-Tof] type mass spectrometer, Triple TOF 5600 + system (SCIEX), using the Information/Data Dependent Acquisition (IDA/DDA) method, and ProteinPilot software (SCIEX) is used to identify the proteins contained in the sample.
The protein identification results will be delivered in the form of electronic data.
The results are generally delivered within about 2 weeks after receiving the sample, but there may be a significant change in the duration depending on the status of the request.
■ Molecular weight measurement of purified proteins using Bruker Ultraflex
The molecular weight of the purified sample that is received will be measured using the matrix-assisted laser dissociation/ionization-Time of flight [MALDI-Tof] mass spectrometer Ultraflex (Bruker).
The measurement results will be delivered in the form of electronic data.
The results are generally delivered within about 2 weeks after receiving the sample, but there may be a significant change in the duration depending on the status of the request.
■ Quantitative analysis with MRM method using Shimadzu LC-MS 8030 plus system
Samples and standard products are kept under custody and the target molecules contained in the samples are quantified by the MRM (Multiple Reaction Monitoring) method using the LC-MS 8030 plus System (Shimadzu Corporation).
It is mandatory to present a detailed measurement protocol using an identical equipment (If the protocol is not provided, we will consider the request as joint research and start by examining the measurement conditions).
The quantitative results will be delivered in the form of electronic data.
The results are generally delivered within about 1 month after receiving the sample, but there may be a significant change in the duration depending on the status of the request.
■ Precise mass measurement, MS/MS fragmentation analysis using Waters Xevo G2-S Q-Tof system
The precise mass and MS/MS fragmentation pattern of the molecules contained in the refined sample kept under custody will be measured with the Quadrupole-Time of flight [Q-Tof] type mass spectrometer Xevo-G2-S Q-Tof system (Waters).
The measurement results will be delivered in the form of electronic data.
The results are generally delivered within about 2 weeks after receiving the sample, but there may be a significant change in the duration depending on the status of the request.
Flow of usage
1) Prior consultation
Before preparing the sample,please send your inquiry to the email address of our laboratory. After adjusting the schedule, we will set up an appointment to discuss the sample preparation method, submission method, and analysis method.
Please note that we cannot accept samples prepared without prior consultation.
2) Preparation and submission of consignment analysis request form and sample sheet （→ Click here for the form）
3) Preparation and submission of samples
4) Delivery of analysis results
Information on the service charges
We will charge based on prescribed standards for the consignment analysis. Please click on the following link for details for consignment analysis charges （→ ：「Rules for the consignment analysis usage charges and internal regulations table of the Medical Research Support Centre」）
Information on collaborative research
We will proceed with collaborative research depending on each individual request. For details, please send your request by email to our laboratory.
Mass Spectrometry Laboratory contact information
Mubanchi, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501
Mass Spectrometry Laboratory, Medical Research Support Center, Graduate School of Medicine, Kyoto University
Phone: 075-753-4424/4418
E-mail: infoms（at）support-center.med.kyoto-u.ac.jp
（* Please replace (at) with @）
*From September 2016, we have been assisting the operations of the Kyoto Biomolecular Mass Spectrometry Society (KBMSS). We request all those who have been using of our laboratory to participate and be a part of this society.（→ Click here for the KBMSS Website）
Formats of various documents
Joint research application form, mass spectrometry laboratory : 
Consignment analysis request form and sample sheet, mass spectrometry laboratory: icon_doc :