Introduction:
This tool is used to annotate compounds from the
LC-MS peak table by matching mz and RT with the public/custom library. The best
top five hits will be shown in the results. If you want to use the custom library
for annotation, a two-column Tab-delimited text file is required with the first
column as compound name and the second column as precise MZ.
Input files:
1.
Raw peak table file in
Tab-delimited txt format, can be obtained from tool "metaMS.runLC".
First column is the compound identifier, the others are samples.
For example:
|
ID |
mz |
rt |
wt15 |
wt16 |
wt18 |
wt19 |
|
LC1 |
589.25 |
41.76407 |
0 |
0 |
0 |
9347.745 |
|
LC2 |
332 |
41.81412 |
0 |
99789.56 |
0 |
0 |
|
LC3 |
246.1 |
41.99718 |
0 |
50669.26 |
0 |
21915.15 |
|
LC4 |
244.1 |
42.03141 |
0 |
35808.77 |
0 |
34583.09 |
|
LC5 |
317 |
42.03826 |
0 |
11905.25 |
0 |
62753.99 |
Parameter:
1.
mz cutoff: A hit that difference
of mz must be <=mz_cutoff.
2.
RT window: The acceptable
retention time difference.
3.
ppm: Parts per million. numeric the relative error for matching peaks that is a
window of user specified error (or the default 10) in ppm for each fragment
mass.
4.
(|M- M0|¡Âm) ¡Á106 (ppm). ¡®M¡¯ is the measured value
of the ion mass; ¡®M0¡¯ is the theoretical value of the ion mass; ¡®m¡¯, an
integer, is the mass of the ion.
5.
For example, the molecular ion
measured value of a compound is 364.2504, the theoretical value is 364.2509,
and the mass measurement accuracy is: |364.2504-364.2509|¡Â364¡Á106=1.4ppm
6.
adducts type: There are several possible adducts and the recommended type that
most commonly occurs is ¡°M+H¡± or ¡°M-H¡±.
Output files:
1.
'identified_pkTable.txt',
identified total peak table file in Tab-delimited txt format, containing
duplicate row names possibly.
For example:
|
ID |
wt15 |
wt16 |
wt18 |
wt19 |
|
[3-(7-hydroxy-4-oxo-4H-chromen-2-yl)phenyl]oxidanesulfonic acid |
0 |
99789.56 |
0 |
0 |
|
2-{[hydroxy(2,3,4-trimethoxyphenyl)methylidene]amino}acetic
acid |
0 |
50669.26 |
0 |
21915.15 |
|
N-Phenylacetyl pyroglutamic acid |
0 |
35808.77 |
0 |
34583.09 |
|
1D-Myo-inositol 1,4-bisphosphate |
0 |
11905.25 |
0 |
62753.99 |
|
Phenytoin |
44555.52 |
95913.45 |
0 |
13436.41 |
2.
'identified_uniq_pkTable.txt',
identified uniq peak table file in Tab-delimited txt
format. When row names are duplication, the row with the maximum intensity will
be retained.
3.
'detailed_information.txt',
detailed information about query and database relationship in library
searching.
Columns are:
|
'Query' |
query name in inputs. |
|
'Query_mz' |
MZ of
the query |
|
'Best_hit' |
name
of the best hit |
|
'Best_hit_adducts_type' |
adducts
type of the best hit |
|
'Best_hits_mz' |
MZ of
the best hit |
|
'Best_hit_delta_mz' |
delta
MZ of the best hit |
|
'Best_hit_rt' |
rt of the best hit |
|
'Best_hit_delta_rt' |
delta rt of the best hit |
|
'Other_hits' |
other
hits in searching |
|
'ther_hits_adducts_type' |
adducts
type of the other hit |
|
'Other_hits_mz' |
Other
hits MZ |
|
'Other_hits_delta_mz' |
delta
MZ of the other hit |
|
'Other_hits_rt' |
Other
hits rt |
|
'Other_hits_delta_rt' |
delta rt of the other hit |
Note:
1. There
is no retention time field in the public
library and only mass spectrum information is used for annotation. For a custom library, this tool supports the joint
annotation by precise MZ and retention time. Users can provide an in-house two-column Tab-delimited text file
with the first column as compound name and the second column as precise MZ.
2. The
tool will identify all possible matching compounds based on all adduct types
selected, sort them according to the matching score, and output them all as
'detailed_information.txt'. Also, the compound with the smallest MZ and RT
deviation will be outputted as the final identified compound in
'identified_pkTable.txt' file.