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b 4 451.2. - 164 805.4. (A). - 164 - 98 707.4. 100. y 1 222.2. (B).  476.5. 100.  632.4. b 7 748.3. PP + H + 165.1.  689.5.  787.5.  730.3. b 7 - 98 650.4. Relative Abundance. 50. (y 6 – 98) 2+ 337.5. Relative Abundance. 50.  787.4. PP + H + 165.1. y 4

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  1. b4 451.2 - 164 805.4 (A) - 164 - 98 707.4 100 y1 222.2 (B)  476.5 100  632.4 b7 748.3 PP + H+ 165.1  689.5  787.5  730.3 b7 - 98 650.4 Relative Abundance 50 (y6 – 98)2+ 337.5 Relative Abundance 50  787.4 PP + H+ 165.1 y4 519.4 - 164 - 98 707.5 - 164 805.3 0 0 200 400 600 800 m/z 200 400 600 800 m/z (– 98)2+ 431.0  470.9 b4 451.2 (C) (E) (D) (– 98)2+ 431.0 (– 98)2+ 430.9 100 100 b4 451.2 100  470.9 NPH + H+ 152.0  194.1 (– 153)2+ 403.4 (– 153)2+ 403.4 b4 451.1 b6 635.3 b7 748.3 y1 211.0 y1 211.0 b7 748.3 (– 153)2+ 403.4  194.1 b6 635.3  470.9 b6 635.3 b5 548.1 b5 548.1 b5 548.1 Relative Abundance Relative Abundance y2 324.3 50 50 Relative Abundance 50 b7 - 98 650.4 y4 508.2 y2 324.3 y2 324.3 y4 508.2 y4 508.3 b7 - 98 650.4 b7 - 98 650.4 y1 211.0 b7 748.2 0 0 0 200 400 600 800 200 400 600 800 200 400 600 800 m/z m/z m/z Supplemental Information SF1. CAD spectra of doubly charged peptide TPpTAPSLG after derivatization with the following reagents: (A) and (B) 1-(2-pyrimidyl)piperazine (PP) with RT 13.2 min (A) and 14.6 min (B), respectively, (C) 2-nitrophenylhydrazine (2-NPH), (D) 3-nitrophenylhydrazine hydrochloride (3-NPH.HCl), and (E) 4-nitrophenylhydrazine (4-NPH).

  2. (B) (– 98)2+ 430.9 100 – 98 860.5 (A) 100  730.4 y4 588.5 y5 659.4 b5 468.3 b7 748.4 Relative Abundance 50  632.5 Relative Abundance 50 b7 - 98 650.5 y4 588.2 b4 371.2 y6 760.4 y4 - 98 490.5 b7 748.2 y1 211.1  940.3 0 200 400 600 800 1000 0 m/z 300 500 700 900 1100 m/z Supplemental Information SF2. CAD spectra of singly (A) and doubly charged (B) peptide TPTAPpSLG after derivatization with 2-nitrophenylhydrazine (2-NPH).

  3. – 153 945.6 (A) 100 b5 575.5  687.5 y4 671.5 y6 898.5  557.5 Relative Abundance 50  y5 785.6  927.7 y3 524.5 b7 832.5 b6 704.5  1081.5 y2 395.5 0 300 500 700 900 1100 m/z b72+ 417.1 b7 832.4 (B) 100 y6 898.4 (-153 - 28)2+ 459.7 y3 524.4 a2 173.2  250.3 y5 785.5 b5 575.4 (-153)2+ 473.6 b2 201.2 50 Relative Abundance  541.3 y2 395.4  558.3 b6 704.4 y1 267.2 y4 671.5  687.4 b3 314.3  815.4 0 200 400 600 800 1000 1200 m/z Supplemental Information SF3. CAD spectra of singly (A) and doubly charged (B) peptide SIINFEKL after derivatization with 2-nitrophenylhydrazine (2-NPH).

  4.    1128.5 (B) (A) (C) 100 100 100 b9 1135.5 y8 1180.5 b9 1000.4 y8 1045.5 b9 + 18 1018.4 b8 1034.4 b8 899.5  1199.6 Relative Abundance Relative Abundance 50 Relative Abundance 50 50  1263.5 y6 725.5 y6 860.5 y8 910.5 b9 1000.5 - 153 1128.5  707.5 b8 899.5 y6 995.5  1111.5 - 153 1263.6 b7 784.5 b7 784.5 b7 784.5 0 0 0 400 600 800 1000 1200 1400 400 600 800 1000 1200 1400 400 600 800 1000 1200 1400 m/z m/z m/z Supplemental Information SF4. CAD spectra of singly charged peptide VHGQPHQDTK: (A) without derivatization, (B) and (C) after derivatization with 2-nitrophenylhydrazine (2-NPH). (B) mono-NPHylation, (C) di-NPHylation.

  5. (A) (-153)2+ 454.2 100 (B) (-153 - 28)2+ 440.5 (-153)2+ 454.1 100 b6 607.4 b6 607.5 b5 494.4 b5 495.4 b8 793.4 y4 566.3  389.2 y4 566.5 b08 - I 662.3 b08 - I 662.4 b8 793.5  521.4  775.5 b82+ 398.0 y2 366.8  775.4 b82+ 397.5  589.3 50 Relative Abundance 50  521.4 Relative Abundance b7 694.5 y1 267.2 b7 694.4 y1 267.5  589.5  388.7  676.4  676.7  250.3  250.6  757.5  757.4 y2 366.4 0 0 200 400 600 800 1000 200 400 600 800 1000 m/z m/z Supplemental Information SF5. CAD spectra of doubly charged peptide EHAGVISVL after derivatization with (A) 3-nitrophenylhydrazine hydrochloride (3-NPH.HCl) and (B) 4-nitrophenylhydrazine (2-NPH).

  6. 1041.5  906.6 (A) (B) 100 100 y7 658.7  676.7  757.4 b8 793.6  757.6  775.5 b6 607.7 50 50 Relative Abundance Relative Abundance b6 607.5  775.7 b7 694.7 b5 494.4 - 153 906.5 b8 793.5 b5 494.5  589.6  888.5  589.4  888.7  476.6  476.3 0 0 300 500 700 900 1100 300 500 700 900 1100 m/z m/z  1041.5  1041.5 (D) (C) 100 100  757.5  757.5  775.6  775.6 - 153 906.6 b6 607.5 50 Relative Abundance 50 Relative Abundance b6 607.5 - 153 906.6 b8 793.6 b5 494.4 b8 793.5 b5 494.4  888.6  888.6  589.4  589.5  476.4  476.4 0 0 300 500 700 900 1100 300 500 700 900 1100 m/z m/z Supplemental Information SF6. CAD spectra of singly charged peptide EHAGVISVL: (A) without derivatization, and after derivatization with (B) 2-nitrophenylhydrazine (2-NPH), (C) 3-nitrophenylhydrazine hydrochloride (3-NPH.HCl), and (D) 4-nitrophenylhydrazine (4-NPH).

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