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500 pmol, 090128_0012, 1-178-01 100 pmol, 090128_0011, 1-178-02 50 pmol, 090128_0010, 1-178-03

1457 1058. 1241 919 112. 1253 964. 1054 834 104. 1403 1014. 1199 899 109. 1565 1128. 1348 999 114. 1535 1095. 1290 947 111. 1658 1146. 1417 1009 109.

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500 pmol, 090128_0012, 1-178-01 100 pmol, 090128_0011, 1-178-02 50 pmol, 090128_0010, 1-178-03

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  1. 1457 1058 1241 919 112 1253 964 1054 834 104 1403 1014 1199 899 109 1565 1128 1348 999 114 1535 1095 1290 947 111 1658 1146 1417 1009 109 1608 1091 1330 941 119 Run on QSTAR Elite, January 2009, summary peptide ID Peptides 99% conf. Proteins 99% conf. after grouping Peptides 95% conf. Peptides 99% conf. Peptides 95% conf. unique unique 500 pmol, 090128_0012, 1-178-01 100 pmol, 090128_0011, 1-178-02 50 pmol, 090128_0010, 1-178-03 10 pmol, 090128_0009, 1-178-04 1 pmol, 090128_0008, 1-178-05 500 fmol, 090128_0007, 1-178-06 100 fmol, 090128_0006, 1-178-07 Peptide identifications with Protein Pilot listing peptides with individual peptide scores > 95% confidence and > 95% confidence also list of unique peptides with individual peptide scores > 95% confidence and > 95% confidence Proteins listed with 99% confidence after grouping (filtering out homolog proteins)

  2. Run on QSTAR Elite, January 2009 (set 1-178) lactoferrin invertase All samples PNGase treated • Depl Plasma + 500 pmol GPS, • Depl Plasma + 100 pmol GPS, • Depl Plasma + 50 pmol GPS, • Depl Plasma + 10 pmol GPS, • Depl Plasma + 1 pmol GPS, • Depl Plasma + 500 fmol GPS, Protein hit # 5 Protein hit # 8 Protein hit # 7 Protein hit # 31 Protein hit # 17 Protein hit # 51 Protein hit # 47 Protein hit # 71 At 10 pmol we first see lactoferrin and invertase as protein hit. The deamidated target peptides then show up at 50, 100, 500 pmol (see next slide)

  3. Lacto(trans)ferrin – positive control (spiked GPS in plasma) QSTAR Elite, Jan. 2009, set 178-1 100 pmol 500 pmol 50 pmol 99 99 99 R.TAGWNIPMGLLFNQTGSCK.F 99 98 96 GLLFNQTGSCK.F Tryptic cleavage occurs R.TAGWNVPIGTLRPFLNWTGPPEPIEAAVAR.F LNWTGPPEPIEAAVAR.F 99 PFLNWTGPPEPIEAAVAR.F 99 LRPFLNWTGPPEPIEAAVAR.F 99 99 99 PFLNWTGPPEPIEAA 99 R.TAGWNVPIGTLR 96 99 99 99 99 R.TAGWNVPIGTLRPF N deamidated Asn Search scores from Protein Pilot

  4. Run on QSTAR Elite, January 2009 • depl plasma + 500 pmol GPS, PNGaseF-treated • (file: 090128_0012, sample 1-178-01) • depl plasma + 100 pmol GPS, PNGaseF-treated • (file: 090128_0011, sample 1-178-02) • depl plasma + 50 pmol GPS, PNGaseF-treated • (file: 090128_0010, sample 1-178-03) • depl plasma + 10 pmol GPS, PNGaseF-treated • (file: 090128_0009, sample 1-178-04) • depl plasma + 1 pmol GPS, PNGaseF-treated • (file: 090128_0008, sample 1-178-05) • depl plasma + 500 fmol GPS, PNGaseF-treated • (file: 090128_0007, sample 1-178-06) • depl plasma + 100 fmol GPS, PNGaseF-treated • (file: 090128_0006, sample 1-178-07)

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