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Figure S1. The workflow of the enrichment of low-abundance endogenous peptides from human urine and mouse brain by double-sided mag-graphene@mSiO2

Figure S2 Mass spectra of 5 nM of standard peptide (Angiotensin II: Molecular Weight = 1046.2, singly charged) eluted by different concentration of ammonia water. a) eluted by 0.4M of ammonia water; b) eluted by 1 M of ammonia water; c) eluted by 2 M of ammonia water; d) eluted by 0.1% TFA/ACN solution. The signal derived from standard peptide is marked with asterisk. Due to the increase of the elution concentration, the silica of the material surface will be dissolved and influence the detection of target molecules. (Fig S1 a-c) And experimental results showed that acidic elution would not attain the performance. (Fig S1d)

Figure S3 Mass spectra of 5 nM of standard peptides (Angiotensin II: Molecular Weight = 1046.2) enriched by different amounts of magnetic graphene double-sided mesoporous silica composites. a)5 μL, 10mg/mL, in water; b) 10 μL, 10mg/mL, in water; c) 15 μL, 10mg/mL, in water; d) 20 μL, 10 mg/mL, in water.

Figure S4 Mass spectra of standard peptides (Angiotensin II: Molecular Weight = 1046.2) a)10 nM, b) 1 nM, c) 0.1 nM enriched by magnetic graphene double-sided mesoporous silica composites (10μL, 10mg/mL, in water). The signal derived from standard peptide is marked with asterisk.

Figure S5 The results of reproducibility test a) the first time, b) the second time, c) the third time, d) the fourth time, e) the fifth time enriched by magnetic graphene double-sided mesoporous silica composites.

Figure S6 Mass spectra of 1mg/ml standard peptides (Angiotensin II: Molecular Weight = 1046.2) enriched by magnetic graphene double-sided mesoporous silica composites (2μL, 10mg/mL, in water). a) Before the enrichment (S/N is 8254.54 and the concentration is 1mg/ml, 200μL) b) the supernatant after the enrichment (S/N is 5942.44 and the calculated concentration is 0.721 mg/mL, 200μL) c) the eluent after the enrichment (S/N is 5478.31 and the calculated concentration is 0.664 mg/mL, 80μL) The max loading capacity and the elution rate are calculated to be 2.79 mg/mg and 95.2%, respectively.

Table S1. Peptides of BSA digest is enriched by magnetic graphene double-sided mesoporous silica composites and identified by MALDI-TOF MS. (score 73, database Swiss-Prot, Protein sequence coverage: 22%, Peptide Mass Tolerance: ± 0.1 Da, Max Missed Cleavages: 1,no modifications)

Table S2. Peptides of MYO digest is enriched by magnetic graphene double-sided mesoporous silica composites and identified by MALDI-TOF MS. (score 87, database Swiss-Prot, Protein sequence coverage: 55%, Peptide Mass Tolerance: ± 0.1 Da, Max Missed Cleavages: 1,no modifications)

Table S3. All peptides of mouse brain enriched by magnetic graphene double-sided mesoporous silica composites and identified by 1D nano-ESI-LC/MS/MS.

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