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1 Supplementary information: Monitoring changes of docosahexaenoic acid-containing lipids during the recovery process of traumatic brain injury in rat using mass spectrometry imaging Shuai Guo 1, Dan Zhou 1, Mo Zhang 1, Tiejun Li 2, Yujie Liu 1, Yupin Xu 1, Tianjing Chen 1 & Zhili Li 1,* 1 Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, PR China 2 School of Pharmacy, Second Military Medical University, Shanghai, PR China *Corresponding author: Zhili Li, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing , PR China. lizhili@ibms.pumc.edu.cn, Tel/Fax:

2 Figure S1. Physical photo of the LE-ESSI. 2

3 Figure S2. Optimizing nebulizing gas flowrate and the distance between spray tip and MS inlet using a PC(36:0) solution (3.2 fmol/μl) as a test sample. Mss spectra (A) and averaged signal intensities of PC(36:0) (B) at the different nebulizing gas flowrate. Mass spectra(c) and averaged signal intensities (D) at the different distances between pray tip and MS inlet. The liquid bridge was put into in a cup containing PC(36:0) solution. Error bars represent the standard deviation in triplicates in (B) and (D). The optimal conditions were marked with red asterisks. 3

4 Figure S3. Optimizing the nebulizing gas flowrate and the distance between spray tip and MS inlet using a homogeneous liver tissue as a test sample. Mass spectra (A) and averaged total ion currents (TIC) (B) of liver tissue at different nebulizing gas flowrate. Mass spectra (C) and averaged TIC (D) versus the different distances between pray tip and MS inlet. The homogeneous mouse liver tissue was imaged by the LE-ESSI at a speed of 100 μm/s, and acquisition time of one spectrum was 1.5 s. Error bars represent the standard deviation of ~80 spectra in (B) and (D). The optimal conditions were marked with red asterisks. 4

5 Figure S4. In situ MS/MS of LPG(22:6), LPE(22:6), PE(P-18:0/22:6), PE(18:0/22:6), and PS(18:0/22:6) on rat brain tissue sections. 5

6 Figure S5. Ion images of the second and third TBI groups at 0, 1, 3, 5, and 7 days after injury. 6

7 Figure S6. (A) Ion images of DHA at the different time points. (B) The image areas of DHA at the different time points. Area circled with yellow line represents the injury area. 7

8 Table S1. Identified analytes on rat brain sections by LE-ESSI-FTICR MS in negative ion mode. Assignment MS/MS fragments m/z Measured Calculated Error Molecular m/z m/z (ppm) Ion form Compound Theoretical m/z Sample m/z formula [M-H] - FA(16:1) C16H30O [M-H] - FA(16:0) C16H32O [M-H] - Inosine C10H12N4O [M-H] - FA(18:2) C18H32O [M-H] - FA(18:1) C18H34O [M-H] - FA(18:0) C18H36O [M+Cl] - Inosine C10H12N4O [M-H] - FA(20:4) C20H32O [M-H] - Sialic acid C11H19NO [M-H] - FA(20:1) C20H38O [M+Cl] - FA(18:1) C18H34O [M-H] - FA(22:6) C22H32O [M-H] - FA(22:4) C22H36O [M+Cl] - FA(20:4) C20H32O [M-H] - Adenosine C10H14N5O7P monophosphate [M-H] - Guanosine C10H14N5O8P monophosphate [M+Cl] - FA(22:6) C22H32O [M+Cl] - MG(16:0) C19H38O [M+Cl] - MG(18:1) C21H40O [M+Cl] - FA(22:5) C24H38O [M+Cl] - MG(20:4) C23H38O [M-H] - LPA(18:1) C21H41O7P [M+Cl] - MG(22:6) C25H38O [M-H] - LPE(18:1) C25H38O / /

9 [M-H] - LPE(20:4) C25H44NO7P / / [M-H] - LPG(18:1) C24H47O9P [M-H] - LPE(22:6) C27H44NO7P / / [M-H] - LPG(20:4) C26H45O9P / / [M-H] - LPS(20:4) C26H44NO9P [M-H] - LPG(22:6) C28H45O9P / / [M-H] - Adenosine C15H23N5O14P2 diphosphate ribose [M-H20-H] - DG(33:2) C36H66O [M-H] - LPS(22:6) C28H44NO9P [M+Cl] - Cer(d34:1) C34H67NO [M-H20-H] - DG(35:3) C38H68O [M+Cl] - Cer(d36:2) C36H69NO [M-H] - LPI(18:0) C27H53O12P [M-H] - LPI(20:4) C29H49O12P / / [M+Cl] - DG(34:2) C37H68O [M-H] - LPA(32:1) C35H68O7P [M-H] - PA(34:1) C37H71O8P [M+Cl] - DG(38:4) C41H72O [M-H] - PA(18:1/18:1) C39H73O8P / / [M-H] - PE(P-34:1) C39H76NO7P [M-H] - PA(18:1/18:0) C39H75O8P / / / / / / / / / [M-H] - LPG(32:1) C38H74O9P [M-H] - PA(37:4) C40H71O8P [M-H] - PE(34:1) C39H76NO8P [M-H] - PA(38:6) C41H69O8P [M+Cl] - PE-Cer(36:2) C38H75O10P [M-H] - PE(P-36:4) C41H74NO7P [M-H] - PE(P-36:2) C41H78NO7P [M-H] - PE(P-36:1) C41H80NO7P 9

10 [M-H] - PA(39:6) C42H71O8P [M+Cl] - PA(36:2) C39H73O8P [M-H] - PE(18:1/18:1) C41H78NO8P / / [M-H] - PE(36:1) C41H80NO8P [M-H] - PE(P-38:6) C43H74NO7P [M-H] - PG(18:0/16:1) C40H77O10P / / / / / / [M-H] - PG(34:0) C40H79O10P [M-H] - PE(P-18:0/20:4) C43H78NO7P / / / / / / [M-H] - PE(P-38:2) C43H82NO7P [M-H] - PS(34:1) C40H76NO10P [M-H] - PE(38:6) C43H74NO8P [M-H] - PE(18:0/20:4) C43H78NO8P / / / / / / / / [M-H] - PG(36:4) C42H75O10P / / / / [M-H] - PS(35:3) C41H74NO10P [M-H] - PE(P-18:0/22:6) C45H78NO7P / / / / / / [M-H] - PG(36:0) C42H83O10P [M-H] - PE(P-18:0/22:4) C45H82NO7P / / [M-H] - PS(18:1/18:1) C42H78NO10P / / / / / / / / [M-H] - PS(18:0/18:1) C42H80NO10P / / / / / / / / / / [M-H] - PE(18:0/22:6) C45H78NO8P / / / / / / / / / / [M+Cl]- PC(16:0/18:1) C42H82NO8P / / / / / / [M-H] - PG(18:0/20:4) C44H79O10P / / [M-H] - PS(38:5) C44H76NO10P [M-H] - PS(18:0/20:4) C44H78NO10P / / / /

11 / / / / [M-H] - PS(38:2) C44H82NO10P [M-H] - PS(P-40:6) C46H78NO9P [M-H] - PG(40:7) C46H77O10P [M+Cl]- PG(P-38:2) C44H83O9P [M+Cl]- PC(18:1/18:0) C44H86NO8P / / / / [M-H] - PS(18:0/22:6) C46H78NO10P / / / / / / / / / / / / / / [M-H] - PS(18:0/22:4) C46H82NO10P / / / / / / / / / / [M-H] - PI(16:0/20:4) C45H79O13P / / / / / / / / [M-H] - PG(44:12) C50H75O10P [M-H] - PS(44:12) C50H74NO10P [M-H] - PI(38:6) C47H79O13P [M-H] - PS(44:10) C50H78NO10P [M-H] - PI(18:1/20:5) C47H81O13P / / / / / / / / [M-H] - PI(18:0/20:4) C47H83O13P / / / / / / / / / / / / [M-H] - PI(40:6) C49H82O13P [M-H] - PIP(P-37:2) C46H85O15P Some metabolites were not confirmed by MS/MS. 11

12 Table S2. Comparison of DHA and DHA-containing lipid species in normal control and TBI rats at 0, 1, 3, 5, and 7 days after the injury. Lipids Kruskal-Wallis test Summary NC vs.d0 NC vs.d1 NC vs.d3 NC vs.d5 NC vs.d7 D0 vs.d1 D0 vs.d3 D0 vs.d5 D0 vs.d7 D1 vs.d3 D1 vs.d5 D1 vs.d7 D3 vs.d5 D3 vs.d7 D5 vs.d7 FA(22:6) *** * *** *** *** *** *** *** *** ns *** *** *** ns ns * LPE(22:6) *** *** *** *** ns ns ns ns *** *** ns *** *** *** *** ns LPG(22:6) *** ns *** * *** *** *** ns *** *** *** *** *** *** *** ns PE(P-18:0/22:6) *** ns *** *** *** *** *** *** *** ns * ns *** ns ns *** PE(18:0/22:6) *** ns *** *** *** *** *** *** *** *** ** ns * ns ns ns PS(18:0/22:6) *** *** *** *** *** *** *** ** ns ns ** *** *** ns * ns NC: normal control. D0, D1, D2, D3, D5, and D7 represent 0, 1, 2, 3, 5, and 7 days, respectively. *, p <0.05; **, p <0.01; ***, p < ns: no significant difference. 12

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