Background
Methods
Chemicals
Urine samples
Sample preparation
LC-ESI-IT MS
Integration procedure
Bioinformatic data analysis
Results
Generating a valid metabolic profile
No. | [MH+] | RT | Metabolite | R2
| RSD [%] | Symbol | Metabolic pathway#
|
---|---|---|---|---|---|---|---|
1
| 302 | 3.0 | 1-ribosyl-3-methyl-5-(2-aminocarboxyethyl)-imidazolium | 0.9875 | 7.4 |
M-1
| (H) |
2
| 247 | 4.3 | Dihydrouridine | 0.9855 | 6.0 |
DHU
| R |
3
| 245 | 4.5 | Pseudouridine | 0.9889 | 3.3 |
Ψ
| R |
4
| 212 | 5.0 | 1-ribosyl-pyridinium | 0.9771 | 5.7 |
M-2
| (N) |
5
| 244 | 6.5 | Cytidine | 0.9815 | 12.0 |
C
| R |
6
| 346 | 7.0 | 3-(3-aminocarboxypropyl)-uridine | 0.9957 | 3.5 |
acp
3
U
| R |
7
| 302 | 7.0 | 5-carbamoylmethyluridine | 0.9977 | 4.0 |
ncm
5
U
| R |
8
| 228 | 7.5 | 1-ribosyl-3-hydroxy-pyridinium | 0.9932 | 2.1 |
M-3
| (N) |
9
| 245 | 8.5 | Uridine | 0.9981 | 8.4 |
U
| R |
10
| 258 | 9.5 | 3-methylcytidine | 0.9787 | 2.7 |
m
3
C
| R |
11
| 259 | 10.5 | 1-ribosyl-4-carbamoyl-5-amino-imidazole | 0.9942 | 6.0 |
AICA riboside
| N |
12
| 282 | 12.0 | 1-methyladenosine | 0.9949 | 3.1 |
m
1
A
| R |
13
| 271 | 14.0 | 1-ribosyl-5-carbamoyl-2-oxo-pyridine | 0.9903 | 3.7 |
2,5-PCNR
| N |
14
| 298 | 17.5 | 7-methylguanosine | 0.9727 | 10.2 |
m
7
G
| R |
15
| 269 | 18.0 | Inosine | 0.9911 | 3.0 |
I
| R |
16
| 271 | 20.5 | 1-ribosyl-3-carbamoyl-4-oxo-pyridine | 0.9955 | 2.1 |
3,4-PCNR
| N |
17
| 296 | 21.5 | 1, N6-dimethyladenosine | 0.9959 | 2.9 |
m
6
1
A
| R |
18
| 259 | 23.5 | 3-methyluridine | 0.9972 | 3.0 |
m
3
U
| R |
19
| 384 | 24.5 | N6-succinyloadenosine | 0.9568 | 11.3 |
N
6
-SAR
| P |
20
| 285 | 25.0 | Xanthosine | 0.9974 | 4.0 |
X
| R |
21
| 385 | 27.5 | S-adenosylhomocysteine | 0.9926 | 4.4 |
SAH
| MP |
22
| 283 | 29.0 | 1-methylinosine | 0.9969 | 3.8 |
m
1
I
| R |
23
| 298 | 31.0 | 1-methylguanosine | 0.9920 | 4.5 |
m
1
G
| R |
24
| 293 | 32.0 | ? | 0.9918 | 14.9 |
293
| ? |
25
| 286 | 32.5 | N4-acetylcytidine | 0.9934 | 7.6 |
ac
4
C
| R |
26
| 298 | 33.5 | 2-methylguanosine | 0.9979 | 8.2 |
m
2
G
| R |
27
| 376 | 34.5 | 9-ribosyl-6-taurinopurine | 0.9974 | 6.2 |
M-4
| (R) |
28
| 398 | 40.0 | 2-methylthio-N6-(cis-hydroxyisopentenyl)-adenosine | 0.9983 | 4.5 |
ms
2
io
6
A
| R |
29
| 326 | 41.0 | N2, N2,7-trimethylguanosine | 0.9911 | 2.7 |
m
2,2,7
G
| R |
30
| 312 | 41.5 | N2, N2-dimethylguanosine | 0.9925 | 4.7 |
m
2
2
G
| R |
31
| 333 | 42.5 | 5-methoxycarbonylmethyl-2-thiouridine | 0.9981 | 4.6 |
mcm
5
s
2
U
| R |
32
| 413 | 46.5 | N6-threonylcarbamoyladenosine | 0.9963 | 3.5 |
t
6
A
| R |
33
| 298 | 48.0 | 5'-deoxy-5'-methyl-thioadenosine | 0.9987 | 13.3 |
MTA
| MP |
34
| 427 | 49.5 | N6-methyl-N6-threonylcarbamoyladenosine | 0.9920 | 5.5 |
m
6
t
6
A
| R |
35
| 459 | 50.0 | 2-methylthio-N6-threonylcarbamoyladenosine | 0.9887 | 3.9 |
ms
2
t
6
A
| R |
Proof of reproducibility
Proof of linearity
Feature selection with best classification performance
No. | encoding* | metabolite ratio | No. | encoding | metabolite ratio |
---|---|---|---|---|---|
1
| arctan (1/7)* | M-1/ncm5U |
23
| arctan (20/3) | X/ψ |
2
| arctan (1/12) | M-1/m1A |
24
| arctan (20/35) | X/ms2t6A |
3
| arctan (2/21) | DHU/SAH |
25
| arctan (21/30) | SAH/m2
2G |
4
| arctan (3/18) | Ψ/m3U |
26
| arctan (22/30) | m1I/m2
2G |
5
| arctan (5/7) | C/ncm5U |
27
| arctan (23/18) | m1G/m3U |
6
| arctan (5/11) | C/AICA riboside |
28
| arctan (25/5) | ac4C/C |
7
| arctan (6/18) | acp3U/m3U |
29
| arctan (25/10) | ac4C/m3C |
8
| arctan (6/19) | acp3U/N6-SAR |
30
| arctan (25/22) | ac4C/m1I |
9
| arctan (8/23) | M-3/m1G |
31
| arctan (26/28) | m2G/ms2io6A |
10
| arctan (9/21) | U/SAH |
32
| arctan (26/30) | m2G/m2
2G |
11
| arctan (11/5) | AICA riboside/C |
33
| arctan (27/13) | M-4/2,5-PCNR |
12
| arctan (11/33) | AICA riboside/MTA |
34
| arctan (28/19) | ms2io6A/N6-SAR |
13
| arctan (12/10) | m1A/m3C |
35
| arctan (29/34) | m2,2,7G/m6t6A |
14
| arctan (12/18) | m1A/m3U |
36
| arctan (29/35) | m2,2,7G/ms2t6A |
15
| arctan (13/9) | 2,5-PCNR/U |
37
| arctan (30/21) | m2
2G/SAH |
16
| arctan (13/20) | 2,5-PCNR/X |
38
| arctan (31/2) | mcm5s2U/DHU |
17
| arctan (14/21) | m7G/SAH |
39
| arctan (31/24) | mcm5s2U/293 |
18
| arctan (14/26) | m7G/m2G |
40
| arctan (33/11) | MTA/AICA riboside |
19
| arctan (16/22) | 3,4-PCNR/m1I |
41
| arctan (33/17) | MTA/m6
1A |
20
| arctan (18/10) | m3U/m3C |
42
| arctan (33/34) | MTA/m6t6A |
21
| arctan (18/21) | m3U/SAH |
43
| arctan (34/12) | m6t6A/m1A |
22
| arctan (19/30) | N6-SAR/m2
2G |
44
| arctan (34/19) | m6t6A/N6-SAR |
Validation | Sensitivity [%] | Specifity [%] | MCC* | TP | FN | TN | FP | p-value |
---|---|---|---|---|---|---|---|---|
CV (10 fold) | 83.5 | 90.6 | 0.743 | 71 | 14 | 77 | 8 | 2.2 × 10-16
|
LOO | 83.5 | 85.9 | 0.694 | 71 | 14 | 73 | 12 | 2.2 × 10-16
|