LC-MS Based tRNA Modification Analysis Service

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Arraystar LC-MS tRNA Modification Analysis Service analyzes 55 nucleoside modifications and characterizes global modification profile of tRNAs as tRNA biochemical properties vital to tRNA biogenesis, structure, functioning and implication in diseases.


• Quantitative analysis of complex tRNA modifications from total RNA samples.
• Full service sample-to-data - from sample QC, tRNA isolation, nucleoside analyte preparation, LC-MS/MS data acquisition, analysis to report.
• High Performance - Highly optimized experimental procedures, state-of-the-art LC-MS system, expertise in operation.
• Best analytical coverage - Simultaneous profiling of 55 nucleoside modifications in tRNAs.

Service Order Guide

1. Check if your modifications of interest are in our standard detection list
2. Read our RNA Submission Guide to make sure your samples are qualified for submission.
3. Click “Add To Cart” below and make your payment online.
4. Fill out the Project Information Sheet and send your samples to Arraystar following the Online Ordering Directions for LC-MS Services.

* We offer bulk order pricing, $335/sample for 1-2 test, $325/sample for 3-10 tests, $315/sample for 11-20 tests, $305/sample for 21-30 tests, $295/sample for 31-50 tests, and $285/sample for >50 tests. 

Service NameCatalog NoSizePrice
LC-MS tRNA Modification Analysis Service- Eukaryotic AS-LC-t-S 1 sample
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Total RNA Extraction Service AS-RE-S 1 sample
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tRNAs are the fundamental component of mRNA decoding and protein translation. tRNAs undergo by far the greatest number of and the most chemically diverse post-transcriptional modifications. These modifications are critical for all core aspects of tRNA function, such as folding, stability and decoding[1]. Typically, modifications in the main body of tRNA are crucial for tRNA structure folding, stability, rigidity and flexibility, whereas modifications in the anticodon loop affect decoding by open loop structure, codon-anticodon pairing, wobbling, and preventing translational frameshifts. Additionally, modified nucleosides serve as identity determinants for aminoacyl-tRNA synthetase (AARS) for extra amino acid recognition accuracy[2]. In general, hypomodified tRNAs are targeted for degradation. Studying tRNA modification is perhaps just as important as tRNA expression profiling.

Defects in tRNA modifications and modification enzymes are linked with human diseases such as cancers, diabetes, neurological syndromes, cardiac conditions, and mitochondrial-linked disorders (Fig. 1)[3]. Analysis of tRNA modification profiles is key to establish the link with the disease, tRNA modification enzymes, and tRNA molecular functioning.

Arraystar LC-MS tRNA Modification Analysis Service offers the sample-to-data solution for simultaneous profiling of 36 nucleosides modifications important to tRNA, using total RNA as the starting material. The service includes tRNA isolation from the total RNA, complete hydrolysis, and dephosphorylation to prepare single nucleosides. The state of the art, ultra high performance LC-MS system delivers a new level of sensitivity, precision, accuracy, dynamic range, and robustness of the quantification results.

tRNA modificationsin human diseases

Figure 1. tRNA modifications in human diseases

1. Kirchner S. and Z. Ignatova (2015) "Emerging roles of tRNA in adaptive translation, sig-nalling dynamics and disease." Nat. Rev. Genet. 16(2):98-112 [PMID: 25534324]
2. El Yacoubi B. et al. (2012) "Biosynthesis and function of posttranscriptional modifications of transfer RNAs." Annu. Rev. Genet. 46:69-95 [PMID: 22905870]
3. Torres A.G. et al. (2014) "Role of tRNA modifications in human diseases." Trends Mol Med 20(6):306-14 [PMID: 24581449]

Table1. Nucleoside modifications profiled by Arraystar LC-MS tRNA Modification Analysis

Number Nucleoside Symbol Number Nucleoside Symbol
1 3'-O-methyladenosine 3'-OMeA 2 3'-O-methyluridine 3'-OMeU
3 2'-O-methylcytidine Cm 4 5-methyl-2-thiouridine m5s2U
5 3-methylcytidine m3C 6 5-methoxyuridine mo5U
7 5-methylcytidine m5C 8 pseudouridine
9 N6-isopentenyladenosine i6A 10 2'-O-methylinosine Im
11 5,2'-O-dimethylcytidine m5Cm 12 3-methyluridine m3U
13 1-methyladenosine m1A 14 1-methylpseudouridine m1
15 2-thiocytidine s2C 16 5-hydroxymethylcytidine hm5C
17 N2, N2, 7-trimethylguanosine m2,2,7G 18 5,2'-O-dimethyluridine m5Um
19 N4-acetyl-2'-O-methylcytidine ac4Cm 20 N6-threonylcarbamoyladenosine t6A
21 N6-methyladenosine m6A 22 2-methylthio-N6-threonylcarbamoyladenosine ms2t6A
23 3'-O-methylcytidine 3'-OmeC 24 5-carboxymethyluridine cm5U
25 2'-O-methyladenosine Am 26 5-methoxycarbonylmethyl-2-thiouridine mcm5s2U
27 N2, N2-dimethylguanosine m22G 28 5-Methoxycarbonylmethyluridine mcm5U
29 5'-O-methylthymidine 5'-OMeT 30 2-methylthio-N6-isopentenyladenosine ms2i6A
31 2'-O-methyluridine Um 32 Peroxywybutosine o2w
33 inosine I 34 5-taurinomethyl-2-thiouridine tm5s2U
35 2'-O-methylguanosine Gm 36 5-oxyacetic acid uridine cmo5U
37 1-methylguanosine m1G 38 5-carbamoylmethyuridine ncm5U
39 7-methylguanosine m7G 40 Queuosine Q
41 N2-methylguanosin m2G 42 5-taurinomethyluridine tm5U
43 3'-O-methylinosine 3'-OMeI 44 5-formyl-2'-O-methylcytidine f5Cm
45 2-thiouridine s2U 46 dihydrouridine D
47 4-thiouridine s4U 48 5-formylcytidine f5c
49 5-methyluridine m5U 50 wybutosine W
51 N4-acetylcytidine ac4C 52 5-methoxycarbonylmethyl-2'-o-methyluridine mcm5Um
53 N6, O2'-methyladenosine m6Am 54 5-methylaminomethyl-2-thiouridine mnm5s2U
55 5-hydroxyuridine ho5U      

Arraystar LC-MS tRNA Modification Analysis

Workflow of Arraystar LC-MS tRNA Modification Analysis.

• Raw and normalized peak data

Raw and normalized peak data

• Total Ion Current chromatogram of nucleosides

Total Ion Current chromatogram of nucleosides

• Differential modification of nucleosides among samples

Differential modification of nucleosides among samples


1. Kirchner S, Ignatova Z. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nature reviews Genetics 2015;16:98-112.
2. El Yacoubi B, Bailly M, de Crecy-Lagard V. Biosynthesis and function of posttranscriptional modifications of transfer RNAs. Annual review of genetics 2012;46:69-95.
3. Torres AG, Batlle E, Ribas de Pouplana L. Role of tRNA modifications in human diseases. Trends in molecular medicine 2014;20:306-14.

Unconventional secretion of Magnaporthe oryzae effectors in rice cells is regulated by tRNA modification and codon usage control. Li G, et al. Nature Microbiology, 2023

Elp3-mediated codon-dependent translation promotes mTORC2 activation and regulates macrophage polarization. Chen D,et al. The EMBO Journal, 2022

Phytophthora capsici infection causes dynamic alterations in tRNA modifications and their associated gene candidates in black pepper. Usha A,et al. Computational and Structural Biotechnology Journal, 2022

Loss of tRNA-modifying enzyme Elp3 activates a p53-dependent antitumor checkpoint in hematopoiesis. Rosu A, et al. Journal of Experimental Medicine, 2021

Elongator Subunit 3 (Elp3) Is Required for Zebrafish Trunk Development. Rojas-Benítez D, et al. International Journal of Molecular Sciences, 2020

Papillary Renal Cell Carcinomas Rewire Glutathione Metabolism and Are Deficient in Both Anabolic Glucose Synthesis and Oxidative Phosphorylation. Ahmad A A, et al. Cancers, 2019

Elongator and codon bias regulate protein levels in mammalian peripheral neurons. Goffena J, et al. Nature Communications, 2018