ms-parser

parsers for MS data

sampleType:

Name	Assay	Meaning	Notes
Check	BA, SCFA	Matrix-free solution of the standard (e.g., 17 BA) set to a certain concentration (e.g., 50 nM). This is used to check the system performance. Remove from any analysis
Condition	BA	LTRs injected at the beginning of the run to stabilise the column before the study sample begins. The value is often not stable. Remove from Analysis and also remove from LTR check
SB	SCFA	Single blank (blank that has undergone sample preparation)
Blank
Calibration		prepared from parent liquid solution of each assay metabolites
LTR
SLTR
VLTR
QC		Quality check solution (prepared from parent liquid solution of each assay metabolites)
PQC		Pooled quality check sample (pooled from samples taken from unhealthy volunteers)

Assays:

Amino Acids

Tryptophan

Bile Acids

Formula	Analyte	Abbrev	MW
C24H36D4O4		CDCA	396.6
C24H36D4O5	Cholic acid (2,2,4,4-D4, 98%)	CA	412.6
C24D4H36O4	Deoxycholic acid (2,2,4,4-D4, 98%)	DCA	396.6
C24H36D4O3	Lithocholic acid (2,2,4,4-D4, 98%)	LCA	380.6
C24H35D5O5	β-Muricholic acid (2,2,3,4,4-D5, 99%)	b-MCA	413.6
C24H36D4O4	Ursodeoxycholic acid (2,2,4,4-D4, 98%) CP 95%	UDCA	396.6
C26H39D4NO5	Glycochenodeoxycholic acid (2,2,4,4-D4, 98%) CP 97%	GCDCA	453.65
C26H39D4NO6	Glycocholic acid (2,2,4,4-D4, 98%) CP 96%	GCA	469.65
C26H39D4NO5	Glycodeoxycholic acid (2,2,4,4-D4, 98%)	GDCA	453.65
C26H39D4NO4	Glycolithocholic acid (2,2,4,4-D4, 98%)	GLCA	437.65
C26H39D4NO5	Glycoursodeoxycholic acid (2,2,4,4-D4, 98%) CP 97%	GUDCA	453.65
C26H40D4NNaO6S	Taurochenodeoxycholic acid, sodium salt (2,2,4,4-D4, 98%) CP 97%	TCDCA	525.71
C26H40D4NaNO7S	Taurocholic acid, sodium salt (2,2,4,4-D4, 98%)	TCA	541.71
C26D4H40NNaO6S	Taurodeoxycholic acid, sodium salt (2,2,4,4-D4, 98%)	TDCA	525.71
C26H40D4NNaO5S	Taurolithocholic acid, sodium salt (2,2,4,4-D4, 98%)	TLCA	509.71
C26H40D4NaNO6S	Tauroursodeoxycholic acid, sodium salt (2,2,4,4-D4, 98%)	TUDCA	525.71

SCFA

Analyte	Standard	MW	Notes
Acetic acid	Acetic acid-d4 (1)
Propionic acid (1)	Propionic acid 13C3 (1)
Isobutyric acid (1)	Isobutyric acid-d7
Butyric acid (1)	Butyric acid-d7 (1)
2Methylbutyric acid (1)
Isovaleric acid	Isovaleric acid-d9 (1)
Valeric acid (1)
3Methylvaleric acid (1)
Hexanoic acid (1)	Hexanoic acid-d11 (1)

Lipids

plate Layout

48 glass vials rack layout:

	1	2	3	4	5	6	7	8
A	Sample	Sample	Sample	Sample	Sample	Sample	SB	QC2
B	Sample	Sample	Sample	Sample	Sample	Sample	Cal5	QC1
C	Sample	Sample	Sample	Sample	Sample	Sample	Cal4	PQC1
D	Sample	Sample	Sample	Sample	Sample	Sample	Cal3	PQC2
E	Sample	Sample	Sample	Sample	Sample	Sample	Cal2	PQC3
F	Sample	Sample	Sample	Sample	Sample	Sample	Cal1	PQC4

96 well plate layout:

	1	2	3	4	5	6	7	8	9	10	11	12
A	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Calibration	QC1
B	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Calibration	QC2
C	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Calibration	QC3
D	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Calibration	QC4
E	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Calibration	LTR
F	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Calibration	LTR
G	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Calibration	LTR
H	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Sample	Calibration	LTR