Table III

MRMaid performance versus experimentally verified transitions taken from Anderson and Hunter (10)

The results shown are derived from MRMaid searches using the default search parameters, namely no internal cleavage sites, 80% of the precursor mass, and 50% of total observations. Peptides that did not meet the criterion of 50% of total observations (shown as red rows in the table of results) were still considered because of the current quantity of available MS/MS reference data. An “observation” in this case is an identification made using a single MS/MS data set that was submitted to GAPP, the results of which have been mined by the MRMaid program. Results are derived from searches performed on August 26, 2008; therefore, the results shown here may have changed because of the increasing volume of data in the GAPP repository. Values are rounded to one decimal place in the table, but MRMaid shows up to three decimal places in the results on the website.

Protein target (Ensembl gene identifier)No. of peptide candidates found for targetPrecursor peptide sequence used by Anderson and Hunter (10)No. times peptide seen in GAPP for targetAverage TS for peptideNo. of predictedb-ions, (1+ only)No. of predictedy-ions (1+ only)RTMS/MS transition (m/z)No. of times product ion seenMean relative intensity for product ion observationsb
Afamin (ENSG00000079557)9DADPDTFFAK943.45521.519.9825.4 (y7)825.37100
940.4 (y8)940.2–940.4735.1
α1-Acid glycoprotein 1 (ENSG00000187681)6NWGLSVYADKPETTK1436.65619.720.71052.5 (y9)1052.3–1052.51391.5
α2-Antiplasmin (ENSG00000167711)5LGNQEPGGQTALK1333.77612.614.9771.4 (y8)771.2–771.413100
α1-Antitrypsin (ENSG00000197249)18DTEEEDFHVDQVTTVK5529.99817.421790.4 (y7)789.9–791.45342.3
889.5 (y8)888.7–890.05396.8
α2-Macroglobin (ENSG00000175899)47LLIYAVLPTGDVIGDSAK2229.111836.528.71059.5 (y11)1059.1–1059.62199.3
1172.6 (y12)1172.2–1172.72025.9
Angiotensinogen (ENSG00000135744)12ALQDQLVLVAAK1336.57523.524.1956.6 (y9)956.3–956.61345.6
713.5 (y7)713.2–713.51220.0
Antithrombin-III (ENSG00000117601)15DDLYVSDAFHK1039.05619.222.3803.4 (y7)803.2–803.41095.1
704.3 (y6)704.1–704.41091.9
Apolipoprotein A-II (ENSG00000158874)3SPELQAEAK137.35412.115546.4 (y5)546.3112
659.4 (y6)659.419
Apolipoprotein E (ENSG00000130203)10LGPLVEQGR748.42515.517.4701.4 (y6)701.2–701.573.7
588.3 (y5)588.2–588.4721.3
β2-Glycoprotein 1 (ENSG00000091583)10ATVVYQGER936.04412.415.4652.3 (y5)652.2–652.38100
Ceruloplasmin (ENSG00000047457)24EYTDASFTNR1040.25514.916.5624.3 (y5)624.2–624.31093
695.3 (y6)695.2–695.41030.8
Clusterin (ENSG00000120885)13LFDSDPITVTVPVEVSR3729.810928.526.31296.7 (y12)1296.3–1297.53627.9
Coagulation factor XIIa heavy chain (ENSG00000131187)8VVGGLVALR944.73619.721.6784.5 (y8)784.4–784.672.1
685.4 (y7)685.3–685.48100
Complement C9 (ENSG00000113600)10AIEDYINEFSVR1337.95628.331.31271.6 (y10)1271.2–1272.21227.1
1027.5 (y8)1027.2–1028.21323
Complement factor H (ENSG00000000971)33SPDVINGSPISQK2334.47616.317.7830.4 (y8)830.1–831.21793.6
572.3 (y5)572.2–572.52330.3
Fibrinogen α chain (ENSG00000171560)16GSESGIFTNTK1540.34714.717.3610.3 (y5)610.1–610.41391.2
780.4 (y7)780.2–781.51531.1
867.5 (y8)867.2–867.51327.1
Fibrinogen β chain (ENSG00000171564)14QGFGNVATNTDGK446.76613.514.6706.3 (y7)706.2–706.5489.3
805.4 (y8)805.3–805.4320.3
Fibronectin (ENSG00000115414)32VTWAPPPSIDLTNFLVR828.134638.230.4977.5 (y8)977.5414
862.5 (y7)862.9–863.235.3
Haptoglobin β chain (ENSG00000197711)7VGYVSGWGR28415518.217.9562.3 (y5)562.1–562.428100
661.3 (y6)661.1–661.42837.9
Histidine-rich glycoprotein (ENSG00000113905)10DSPVLIDFFEDTER2933.77737.727.71171.5 (y9)1171.2–1172.252941.6
1058.4 (y8)1058.032994.3
Hemopexin (ENSG00000110169)15NFPSPVDAAFR3159.53623.620.4959.6 (y9)959.2–960.21492.6
775.3 (y7)775.1–775.5148.6
Heparin cofactor II (ENSG00000099937)11TLEAQLTPR652.45516.418814.4 (y7)814.3–814.45100
685.4 (y6)685.3–685.4534.2
Histidine-rich glycoprotein (ENSG00000113905)10DSPVLIDFFEDTER2933.77737.727.71171.5 (y9)1171.2–1172.22941.6
1058.4 (y8)1058.0–1059.02994.3
Plasma retinol-binding protein precursor (ENSG00000138207)5YWGVASFLQK2747.55635.124.1849.5 (y8)849.2–849.525100
693.4 (y6)693.1–693.52649.4
Plasminogen (ENSG00000122194)16LSSPAVITDK351.00615.317.7743.4 (y7)743.3–743.539.7
830.5 (y8)830.2–830.5314
Prothrombin (ENSG00000180210)16ETAASLLQAGYK1542.46620.220.6879.5 (y8)879.2–879.51555.3
679.4 (y6)679.1–679.41572.8
Serum albumin (ENSG00000163631)30LVNEVTEFAK9849.24619.319.9937.4 (y8)937.1–938.29596.6
694.4 (y6)694.1–694.69321.9
Serum amyloid P-component (ENSG00000132703)7VGEYSLYIGR1253.25621.320.91057.2 (y9)1057.4–1057.51012.6
871.5 (y7)871.3–871.41149.4
Transferrin (ENSG00000091513)32EDPQTFYYAVAVVK3729.28620.325.31160.6 (y10)1160.2–1160.93117.6
1288.7 (y11)1288.0–1289.2174.2
Transthyretin (ENSG00000118271)5AADDTWEPFASGK7838.97722.318.3921.4 (y8)921.1–922.27856.7
606.4 (y6)606.1–606.47799.6
Vitamin D-binding protein (ENSG00000145321)15THLPEVFLSK1434.84619.723.9819.5 (y7)819.2–819.51499.4
932.5 (y8)932.2–932.61459.3
Vitronectin (ENSG00000109072)9DVWGIEGPIDAAFTR4832.79836.442.0947.5 (y9)947.1–948.24284.2
FEDGVLDPDYPR2740.65622.224.9890.5 (y8)890.2–891.24233.8
875.4 (y7)875.1–875.526100
1031.5 (y9)1031.1–1031.8267.8
Zinc α2-glycoprotein (ENSG00000160862)8EIPAWVPFDPAAQITK1329.98836.227.31087.7 (y10)1087.2–1087.61297.5
728.4 (y7)728.2–728.6137.8
  • a These values may be shown as a range to account for the mass tolerance of fragment ions entered by the user when the MS/MS data were submitted to GAPP for analysis.

  • b Relative intensity refers to the fact that signal intensity is normalized by the GAPP analysis pipeline. When spectra are uploaded for protein identification, the y-dimension of each spectrum is normalized to 100. This means that for all the spectra in the GAPP database that are mined by the MRMaid program there is a maximum y value of 100. This is also reflected in the graphical MS/MS spectra displayed on the MRMaid product ion results page. The intensity values differ for each individual peak in each experiment submitted to GAPP; therefore the mean over all observations is given for each particular ion species, for example, y8. It is possible to successfully monitor product ions at low abundance as long as there is no overlap with other peaks: generally there is less likely to be overlap at the very high m/z end of the spectrum; therefore the higher the m/z, the lower the abundance that can be successfully tolerated.