Table I.
A summary of intercross-linked peptides and proteins identified using Rink-based PIR
| Precursor mass | Peptide mass | Identified peptide | Error | Protein of origin | Typea | Molecular mass |
|---|---|---|---|---|---|---|
| Da | Da | ppm | kDa | |||
| 5047.3774 | 1911.9354 | TDNTYPGTKVPTSFAWK | 0.67 | SO1779, decaheme cytochrome c (OmcA) | OM | 79 |
| 1815.8954 | GFALSNSKVSTYNEATK | 2.69 | SO1779, decaheme cytochrome c (OmcA) | OM | 79 | |
| 4916.3157 | 2271.0398 | LMSEDQIKTTFADVAGCDEAK | 1.35 | SO1197, cell division protein (FtsH) | IM | 71 |
| 1325.7302 | NTPVEKGGIGQVK | 3.38 | SO2756, antioxidant | C | 22 | |
| 4906.2116 | 2641.1930 | ASFSGNSDIMVLEPDSEFFKYMK | 5.68 | SO0606, nf protein (HflC) | IM | 33 |
| 945.4501 | DKNTPSER | 1.57 | SO3343, conserved hypothetical protein | OM | 21 | |
| 4884.3531 | 2384.1255 | FNPAKSELTYYLSNNFYDAK | 2.92 | SO0404, hypothetical protein | OM | 130 |
| 1180.6630 | LVYTTTKDLK | 6.56 | SO1778, decaheme cytochrome c (MtrC) | OM | 71 | |
| 4800.2140 | 2384.1324 | FNPAKSELTYYLSNNFYDAK | 3.61 | SO0404, hypothetical protein | OM | 130 |
| 1096.5665 | GFKGFSQAQK | 1.68 | SO1897, isodehydrogenase (Ivd) | C | 42 | |
| 4717.2362 | 2580.3263 | KFGTFTVAETGWPALDPLFIENK | 2.32 | SO4680, conserved hypothetical protein | C | 41 |
| 817.4073 | AWGKDNK | 1.17 | SO1778, decaheme cytochrome c (MtrC) | OM | 71 | |
| 4429.1018 | 1815.8948 | GFALSNSKVSTYNEATK | 3.02 | SO1779, decaheme cytochrome c (OmcA) | OM | 79 |
| 1293.6500 | GLKTDNTYPGTK | 5.01 | SO1779, decaheme cytochrome c (OmcA) | OM | 79 | |
| 4353.0545 | 2222.1268 | SQINPKFQDLLTADVSFSGR | 2.85 | SO0404, hypothetical protein | OM | 130 |
| 811.3956 | FKSGDMK | 7.10 | SO0404, hypothetical protein | OM | 130 | |
| 4256.0728 | 2119.1187 | GKPHVAFSHLIHNVHNANK | 0.02 | SO1778, decaheme cytochrome c (MtrC) | OM | 71 |
| 817.4082 | AWGKDNK | 1.90 | SO1778, decaheme cytochrome c (MtrC) | OM | 71 | |
| 4228.0116 | 524.3454 | LHKK | 2.52 | SO1778, decaheme cytochrome c (MtrC) | OM | 71 |
| 2384.1452 | FNPAKSELTYYLSNNFYDAK | 4.66 | SO0404, hypothetical protein | OM | 130 | |
| 3920.8081 | 1468.7459 | GYQWQAYINAKK | 0.27 | SO1779, decaheme cytochrome c (OmcA) | OM | 79 |
| 1132.535 | EKVGETEADR | 0.99 | SO1779, decaheme cytochrome c (OmcA) | OM | 79 | |
| 3793.8837 | 1293.6629 | GLKTDNTYPGTK | 5.21 | SO1779, decaheme cytochrome c (OmcA) | OM | 79 |
| 1180.6690 | LVYTTTKDLK | 0.88 | SO1778, decaheme cytochrome c (MtrC) | OM | 71 | |
| 3744.775 | 1448.6644 | WNGTDTNSAAEKR | 1.81 | SO1779, decaheme cytochrome c (OmcA) | OM | 79 |
| 976.5662 | AKFSNIGIK | 7.54 | SO1779, decaheme cytochrome c (OmcA) | OM | 79 | |
| 3702.7157 | 1293.6484 | GLKTDNTYPGTK | 6.25 | SO1779, decaheme cytochrome c (OmcA) | OM | 79 |
| 1089.5310 | EVTDEAGNKK | 0.80 | SO2001, 5-nucleotidase (UshA) | OM | 61 | |
| 3440.6819 | 729.3697 | KEYYK | 0.33 | SO3545, OmpA family protein | OM | 40 |
| 1391.7772 | YQQLVKTNAISK | 0.80 | SO4693, type I secretion membrane fusion protein | OM | 40 | |
| 3355.6241 | 1015.5170 | MENPEIKR | 4.94 | SO3064, amidophosphoribosyltransferase (PurF) | C | 56 |
| 1020.5345 | GLSAKAFDGR | 0.62 | SO0243, ribosomal protein L5 | C | 20 | |
| 3300.5526 | 848.4773 | MKSKLDK | 1.98 | SO1854, hypothetical protein | OM | 66 |
| 1132.5320 | EKVGETEADR | 3.29 | SO1779, decaheme cytochrome c (OmcA) | OM | 79 | |
| 3291.5894 | 982.5242 | SKEAANHVK | 4.78 | SO2366, response regulator | C | 59 |
| 989.5303 | EISMNIKR | 2.54 | SO0253, ribosomal protein S13 | C | 13 | |
| 3272.5790 | 937.5061 | IAGSMGFKK | 0.71 | SO0228, translation elongation factor G (FusA-1) | C | 77 |
| 1015.5167 | MENPEIKR | 4.65 | SO3064, amidophosphoribosyltransferase (PurF) | C | 56 | |
| 3246.6089 | 987.5094 | AEFAKTHGK | 4.43 | SO1521, iron-sulfur cluster-binding protein | C | 102 |
| 939.5683 | GKPVWVVR | 3.06 | SO0608, ubiquinol-cytochrome c | IM | 21 | |
| 3218.6457 | 850.4869 | FNTLTKK | 5.01 | SO4410, glutamine synthetase, type I (GlnA) | C | 52 |
| 1048.6404 | IPVVPSPKGR | 1.13 | SO4410, glutamine synthetase, type I (GlnA) | C | 52 | |
| 3179.4984 | 920.4166 | WADKMDR | 0.92 | SO0719, TonB-dependent receptor, putative | OM | 84 |
| 939.5683 | GKPVWVVR | 3.06 | SO0608, ubiquinol-cytochrome c | IM | 21 | |
| 3021.4109 | 811.3898 | FKSGDMK | 0.04 | SO0404, hypothetical protein | OM | 130 |
| 890.4986 | LGVFGKDR | 1.35 | SOA0110, lipoprotein, putative | OM | 150 | |
| 2194.0687 | 437.2634 | KYK | 0.91 | SO4211, preprotein translocase (SecA) | C | 103 |
| 437.2634 | YKK | 0.91 | SO1295, major outer membrane lipoprotein | OM | 9 |
a
Type of identified proteins: OM, IM, and C denote outer membrane, inner membrane, and cytoplasmic proteins, respectively.