mRNA Modification Analysis by MS

Recently, RNA modifications located in the coding region of mRNAs have been regarded as critical regulators of gene expression. However, there are still many aspects related to the functions of these diverse mRNA modifications. We employ mass spectrometry (MS) to provide a comprehensive, accurate and affordable solution for mRNA modification analysis including mapping, quantitation and characterization.


RNAs undergo a variety of modifications, which is a reversible and dynamic process. Multiple chemical modifications, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A) and pseudouridine (Ψ), have been detected within open reading frames (ORFs) of mRNAs. Among them, m6AThese modifications have been implicated with the fate of an mRNA, including its maturation, translation, and decay. For example, RNA m6A can direct mRNAs to distinct fates and accelerate mRNA metabolism and translation. MS offers a direct readout on any modifications that alter the mass of nucleoside and has long been a robust method for detecting, profiling, and characterizing known and unknown mRNA modification, profiling and characterizing modified mRNAs. Based on the LC-MS/MS platform, CD Genomics provides qualitative and quantitative information on all mRNA modifications under certain conditions or in diverse genetic backgrounds. We can help you detect the expression levels of as many as 36 types of modifications in a given sample (Table 1). Our mRNA modification analysis service by MS provides detailed insights into the function of mRNA modifications, mRNA biology and the development of targeted therapies.

Table 1. The list of mRNA modifications we have detected.

Nucleoside Symbol Nucleoside Symbol Nucleoside Symbol
5-methylcytidine m5C 5-hydroxymethylcytidine hm5C 5,2'-O-dimethylcytidine m5Cm
3-methylcytidine m3C 1-methyladenosine m1A N6-methyladenosine m6A
7-methylguanosine m7G 1-methylguanosine m1G N2-methylguanosine m2G
pseudouridine Ψ 1-methylpseudouridine m1Ψ inosine I
2'-O-methylcytidine Cm N6-isopentenyladenosine i6A 3'-O-methyladenosine 3'-OMeA
N4-acetylcytidine ac4C 2-thiocytidine s2C N2,N2,7-trimethylguanosine m2,2,7G
3'-O-methylcytidine 3'-OMeC 2'-O-methyladenosine Am N4-acetyl-2'-O-methylcytidine ac4Cm
4-thiouridine s4U 2'-O-methyluridine Um N2,N2-dimethylguanosine m22G
3'-O-methylinosine 3'-OMeI 2-thiouridine s2U 5'-O-methylthymidine 5'-OMeT
5-methoxyuridine mo5U 3'-O-methyluridine 3'-OMeU 2'-O-methylguanosine Gm
3-methyluridine m3U 3'-O-methylguanosine 3'-OMeG 5,2'-O-dimethyluridine m5Um
5-methyluridine m5U 2'-O-methylinosine Im 5-methyl-2-thiouridine  m5s2U


ExperiencedTranscriptome-WideBioinformatics AnalysisQuality Control
The MS experiment is performed by our experienced expert team.Profile all mRNA modifications, either known or unknown.Data QC; profiling of mRNA modifications; quantitative analysis; functional analysisQuality control is executed following every procedure.

Project Workflow

1. Sample Preparation

RNA isolation from a cell line, tissue, or bacterial colony.

2. mRNA Isolation

Isolate mRNA molecules using sing oligo(dT) beads.

3. mRNA Digestion

Enzymatically digest RNAs into constituent ribonucleosides.

4. Mass Spectrometry

Quantitative measurement of modified ribonucleosides by liquid chromatography tandem mass spectrometry (LC-MS/MS).

Sample Requirements

We work with a wide range of sample types including protein solution, fresh tissue, cultured cells, blood, and microbial colonies. Please feel free to contact us for sample size.

Sample Storage: extracted protein should be stored at -80°C. Avoid repeated freezing and thawing.

Shipping Method: when shipping the sample, it is stored in a 1.5 mL Eppendorf tube, sealed with a sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.

Deliverable: data QC report, MS results, integrated experimental report (materials, methodologies, and bioinformatics analysis).


  1. Hoernes T P, Hüttenhofer A, Erlacher M D. mRNA modifications: Dynamic regulators of gene expression?. RNA biology, 2016, 13(9): 760-765.
  2. Wetzel C, Limbach P A. Mass spectrometry of modified RNAs: recent developments. Analyst, 2016, 141(1): 16-23.
* For Research Use Only. Not for use in diagnostic procedures.

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