Table 2.
Representative false positive peptide identifications in a full tryptic search and the corresponding partial tryptic peptides from abundant serum proteins
| Full Tryptic Search | Partial Tryptic Search | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Spectrum | Xcorr | dCN | Δ Mass | Peptide Sequence | Protein ID | Protein Name | Xcorr | dCn | ΔMass | Peptide Sequence | Protein ID | Protein Name |
| 1.1799 | 2.07 | 0.30 | −7.9 | RALGDPATPTEGPRR | UPI0000D61BBA | UPI0000D61BBA UniRef100 entry | 3.13 | 0.34 | −0.8 | QVDAVPANGQTPIQR | Q60FE4 | Fibronectin 1 |
| 2.3203 | 2.07 | 0.07 | −1 | MTILQTYFR | O75348 | Vacuolar ATP synthase subunit G 1 | 2.72 | 0.14 | −2.5 | TMEQLTPELK | UPI0000D820D0 | apolipoprotein B precursor |
| 4.5842 | 1.87 | 0.06 | −7.8 | MGPLSPARTLRLWGPR | Q96RP7 | Galactose-3-O-sulfotransferase 4 | 4.31 | 0.46 | 1 | GLTPGVEYVYTIQVLR | Q60FE4 | Fibronectin 1 |
| 6.4234 | 1.69 | 0.12 | −3.4 | GTLAAQAPHLCPR | Q59H20 | Hypothetical protein | 3.45 | 0.49 | 0 | AVTADGNAFIGDIK | UPI000014D030 | inter-alpha (globulin) inhibitor H1 |
| 8.7814 | 1.75 | 0.10 | 4.2 | QQLGWEAWLQYSFPLQLEPSAQTWGPGTLR | O00334 | Phosphatidylinositol 3-kinase delta catalytic subunit | 2.28 | 0.07 | 3.1 | SVVPVFYVFHYLETGNHWNIFHSDPLIEK | Q27I61 | Complement component 5 |
| 10.2892 | 2.43 | 0.11 | −6.2 | FSNDNIKHSQNMR | Q96M29 | Tektin-5 | 4.01 | 0.39 | 0.8 | SLCSDQQSHLEFR | UPI000014279E | protein S (alpha) |
| 12.4906 | 1.53 | 0.14 | −3.3 | VDGTRGRGGPAWR | UPI0000DD7E44 | PREDICTED: hypothetical protein | 3.13 | 0.47 | 2.8 | TLTGGNVFEYGVK | Q2TAZ5 | Complement factor H |
| 18.2465 | 2.05 | 0.15 | 0.5 | RDTFNHLTTWLEDAR | P61019 | Ras-related protein Rab-2A | 4.59 | 0.45 | 2.9 | SIPVCGQDQVTVAM*TPR | Q4QZ40 | Prothrombin |
| 19.2373 | 2.56 | 0.07 | −2.8 | SGNRDRTVQSPQSK | Q15695 | U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit | 3.63 | 0.21 | −0.4 | RPQGSCSLEGVEIK | P00751 | Complement factor B precursor |
| 23.4572 | 3.15 | 0.15 | 5.9 | QDMIIDKLNGNSTPEK | Q9NY46 | Sodium channel protein type 3 subunit alpha | 5.77 | 0.45 | −2.6 | PNFNGNTLDNDIMLIK | Promega sequencing grade modified trypsin | |
| 27.1682 | 2.40 | 0.10 | 5.6 | IDEKSLDESKNPAR | Q7RTM1 | Otopetrin-1 | 4.04 | 0.41 | −1.4 | ALSSVQESQVAQQAR | P02656 | Apolipoprotein C-III precursor |
| 27.3208 | 2.55 | 0.14 | 5.5 | EKDEQIRGLMEEGEK | Q59GK0 | TATA element modulatory factor 1 variant | 3.43 | 0.22 | −0.7 | LIHGPNLYCYSDVEK | P02790 | Hemopexin precursor |
| 28.4748 | 2.20 | 0.09 | −2.4 | PGTMMPEAFLQEAQIMKK | UPI0000456B50 | Proto-oncogene tyrosine- protein kinase Yes | 5.03 | 0.46 | −1.9 | LGEHNIDVLEGNEQFINAA | Promega sequencing grade modified trypsin | |
| 29.5703 | 2.36 | 0.09 | −2.8 | KPTEWPLKLVPQHR | Q9P1K3 | PRO1163 | 5.14 | 0.52 | −2 | VLNLPSGVTVLEFNVK | Q27I61 | Complement component 5 |
| 33.3622 | 2.40 | 0.08 | 3.9 | LNESDEQHQENEGTNQLVMGIQK | Q15545 | Transcription initiation factor TFIID subunit 7 | 5.64 | 0.39 | −1.4 | EPTM*YGEILSPNYPQAYPSEVEK | P09871 | Complement C1s subcomponent precursor |
| 39.4095 | 2.40 | 0.07 | 3.6 | GFTVKMHCYMNSASGNVSWLWK | Q53FS2 | CD79B antigen isoform 1 variant | 4.98 | 0.32 | 0.2 | EVSADQVATVM*WDYFSQLSNNAK | P06727 | Apolipoprotein A-IV precursor |
| 36.2075 | 2.86 | 0.07 | 4.1 | SIENDSDEVEERAENFPR | Q8N1H7 | Protein SIX6OS1 | 5.35 | 0.36 | −1.1 | HPNSPLDEENLTQENQDR | P01011 | Alpha-1-antichymotrypsin precursor |