Table S1. Fragmentation Rules and Relative Intensity Rules of Pgpc That Used to Construct

Table S1. Fragmentation rules and relative intensity rules of pGPC that used to construct the fragment ion database.

Fragment Ions / Structural Feature Reflected / Substituent Position
[M+Li]+ / NN / 
[M+Li-59]+ / HG / 
[M+Li-183]+ / HG / 
[M+Li-189]+ / HG / 
[M+Li-R1OH]+ / R1 / 
[M+Li-189-R2CO2H]+ / R2 / 
[M+Li-59-R1OH]+ / R1 / 
[M+Li-59-R2CO2H]+ / R2 / 
[M+Li-103-R’2CHCO]+ / R2 / 
[M+Li-R2CO2Li]+ / R2 / 
[R2CO]+ / R2 / 
[C2H5PO4+Li]+ / HG / 
[C5H12N]+ / HG / 

*The indicated ions can contain information about the following structural features of the phospholipid molecule: NN (Number of Nitrogens); HG (head group); R1 (sn-1 substituent); R2 (sn-2 substituent); substituent position refers to sn-1 vs. sn-2. p means plasmenyl-. Both plasmalogens and 1-O-alkyl ether lipids have an acyl substituent only in the sn-2 position. See reference 20 for future detail.

Table S2. Fragmentation rules and relative intensity rules of aGPC that used to construct the fragment ion database.

Fragment Ions / Structural Feature Reflected / Substituent Position
[M+Li]+ / NN / 
[M+Li-59]+ / HG / 
[M+Li-183]+ / HG / 
[M+Li-189]+ / HG / 
[M+Li-189-R2CO2H]+ / R2 / 
[M+Li-103-R’2CHCO]+ / R2 / 
[M+Li-R2CO2Li]+ / R2 / 
[R1]+ / R1 / 
[R2CO]+ / R2 / 
[C2H5PO4+Li]+ / HG / 
[C5H12N]+ / HG / 

*The indicated ions can contain information about the following structural features of the phospholipid molecule: NN (Number of Nitrogens); HG (head group); R1 (sn-1 substituent); R2 (sn-2 substituent); substituent position refers to sn-1 vs. sn-2. a means plasmanyl-. Both plasmalogens and 1-O-alkyl ether lipids have an acyl substituent only in the sn-2 position. See reference 20 for future detail.

Table S3. Fragmentation rules and relative intensity rules of GPE that used to construct the fragment ion database.

Fragment Ions / Structural Feature Reflected / Substituent Position
[M-H]- / NN / 
[M-H-R1CO2H]- / R1 / +
[M-H-R2CO2H]- / R2 / +
[M-H-R1’CHCO]- / R1 / +
[M-H-R2’CHCO]- / R2 / +
[R1CO2]- / R1 / 
[R2CO2]- / R2 / 
[C5H11NPO5]- / HG / 
[C2H7NPO4]- / HG / 

*The indicated ions can contain information about the following structural features of the phospholipid molecule: NN (Number of Nitrogens); HG (head group); R1 (sn-1 substituent); R2 (sn-2 substituent); substituent position refers to sn-1 vs. sn-2. Positional assignments: [M-H-R1CO2H]- >[M-H-R2CO2H]- , [M-H-R1’CHCO]- >[M-H-R2’CHCO]- . See reference 16 for future detail.

Table S4. Fragmentation rules and relative intensity rules of pGPE that used to construct the fragment ion database.

Fragment Ions / Structural Feature Reflected / Substituent Position
[M-H]- / NN / 
[M-H-R2CO2H]- / R2 / 
[M-H-R2’CHCO]- / R2 / 
[R2CO2]- / R2 / 
[C5H11NPO5]- / HG / 
[C2H7NPO4]- / HG / 

*The indicated ions can contain information about the following structural features of the phospholipid molecule: NN (Number of Nitrogens); HG (head group); R1 (sn-1 substituent); R2 (sn-2 substituent); substituent position refers to sn-1 vs. sn-2. p means plasmenyl-. Both plasmalogens and 1-O-alkyl ether lipids have an acyl substituent only in the sn-2 position. See reference 16 for future detail.

Table S5. Fragmentation rules and relative intensity rules of aGPE that used to construct the fragment ion database.

Fragment Ions / Structural Feature Reflected / Substituent Position
[M-H]- / NN / 
[M-H-R2CO2H]- / R2 / 
[M-H-R2’CHCO]- / R2 / 
[R2CO2]- / R2 / 
[C5H11NPO5]- / HG / 
[C2H7NPO4]- / HG / 

*The indicated ions can contain information about the following structural features of the phospholipid molecule: NN (Number of Nitrogens); HG (head group); R1 (sn-1 substituent); R2 (sn-2 substituent); substituent position refers to sn-1 vs. sn-2. a means plasmanyl-. Both plasmalogens and 1-O-alkyl ether lipids have an acyl substituent only in the sn-2 position. See reference 16 for future detail.

Table S6. Fragmentation rules and relative intensity rules of GPS that used to construct the fragment ion database.

Fragment Ions / Structural Feature Reflected / Substituent Position
[M-H]- / NN / 
[M-H-87]- / HG / 
[M-H-87-R1CO2H]- / R1 / +
[M-H-87-R2CO2H]- / R2 / +
[M-H-87-R1’CHCO]- / R1 / +
[M-H-87-R2’CHCO]- / R2 / +
[R1CO2]- / R1 / 
[R2CO2]- / R2 / 
[C3H6PO5]- / HG / 

*The indicated ions can contain information about the following structural features of the phospholipid molecule: NN (Number of Nitrogens); HG (head group); R1 (sn-1 substituent); R2 (sn-2 substituent); substituent position refers to sn-1 vs. sn-2. Positional assignments: [M-H-87-R1CO2H]-<[M-H-87-R2CO2H]-, [M-H-87-R1’CHCO]-<[ [M-H-87-R2’CHCO]-. See reference 23 for future detail.

Table S7. Fragmentation rules and relative intensity rules of GPA that used to construct the fragment ion database.

Fragment Ions / Structural Feature Reflected / Substituent Position
[M-H]- / NN / 
[M-H-R1CO2H]- / R1 / +
[M-H-R2CO2H]- / R2 / +
[M-H-R1’CHCO]- / R1 / +
[M-H-R2’CHCO]- / R2 / +
[R1CO2]- / R1 / 
[R2CO2]- / R2 / 
[C3H6PO5]- / HG / 

*The indicated ions can contain information about the following structural features of the phospholipid molecule: NN (Number of Nitrogens); HG (head group); R1 (sn-1 substituent); R2 (sn-2 substituent); substituent position refers to sn-1 vs. sn-2. Positional assignments: [M-H-R1CO2H]- <[M-H-R2CO2H]-, [M-H-R1’CHCO]- <[M-H-R2’CHCO]-. See reference 15 for future detail.

Table S8. Fragmentation rules and relative intensity rules of GPG that used to construct the fragment ion database.

Fragment Ions / Structural Feature Reflected / Substituent Position
[M-H]- / NN / 
[M-H-R1CO2H]- / R1 / +
[M-H-R2CO2H]- / R2 / +
[M-H-R1’CHCO]- / R1 / +
[M-H-R2’CHCO]- / R2 / +
[M-H- R1CO2H -74]- / R1 / +
[M-H- R2CO2H -74]- / R2 / +
[R1CO2]- / R1 / 
[R2CO2]- / R2 / 
[C6H12PO7]- / HG / 
[C6H10PO6]- / HG / 
[C3H8PO6]- / HG / 
[C3H6PO5]- / HG / 

*The indicated ions can contain information about the following structural features of the phospholipid molecule: NN (Number of Nitrogens); HG (head group); R1 (sn-1 substituent); R2 (sn-2 substituent); substituent position refers to sn-1 vs. sn-2. Positional assignments: [M-H-R1CO2H]- <[M-H-R2CO2H]- , [M-H-R1’CHCO]- <[M-H-R2’CHCO]- , [M-H- R1CO2H -74]-<[M-H- R2CO2H -74]-. See reference 18 for future detail.

Table S9. Fragmentation rules and relative intensity rules of GPI that used to construct the fragment ion database.

Fragment Ions / Structural Feature Reflected / Substituent Position
[M-H]- / NN / 
[M-H-R1CO2H]- / R1 / +
[M-H-R2CO2H]- / R2 / +
[M-H-R1’CHCO]- / R1 / +
[M-H-R2’CHCO]- / R2 / +
[M-H-R1’CHCO-180]- / R1 / +
[M-H-R2’CHCO-180]- / R2 / +
[R1CO2]- / R1 / 
[R2CO2]- / R2 / 
[C9H16PO10]- / HG / 
[C9H14PO9]- / HG / 
[C6H12PO9]- / HG / 
[C6H10PO8]- / HG / 
[C6H8PO7]- / HG / 
[C3H6PO5]- / HG / 

*The indicated ions can contain information about the following structural features of the phospholipid molecule: NN (Number of Nitrogens); HG (head group); R1 (sn-1 substituent); R2 (sn-2 substituent); substituent position refers to sn-1 vs. sn-2. Positional assignments: [M-H-R1CO2H]- <[M-H-R2CO2H]-, [M-H-R1’CHCO]- <[M-H-R2’CHCO]- , [M-H-R1’CHCO-180]- <[M-H-R2’CHCO-180]- . See reference 17 for future detail.