Table 1.
Comparison of biological triplicate samples of HeLa cells using sugar analog (SAE) and lectin enrichment (LE)
| No. | Identified proteins | UniProtKB | MWa) | Sugar analog | Lectin capture | Summary | |||
|---|---|---|---|---|---|---|---|---|---|
| Avg % Seq Cov (Avg Pepb)) | Avg % Seq Cov (Avg Pepb)) | SAE | LE | ||||||
| −PLC | +PLC | −PLC | +PLC | +PLC | +PLC | ||||
| 1 | CD109 antigen | Q6YHK3 | 162 | 3.2 (4) | 13 (16) | 3.6 (4) | 16.1 (17) | 3/3 | 3/3 |
| 2 | Folate receptor alpha | P15328 | 30 | 4.3 (1) | 35.3 (8) | 7.1 (1) | 27.8 (6) | 3/3 | 3/3 |
| 3 | Alkaline phosphatase, tissue-nonspecific isozyme | P05186 | 57 | 6.3 (2) | 28.9 (12) | 11.5 (4) | 39.6 (16) | 3/3 | 3/3 |
| 4 | Complement decay-accelerating factor | P08174 | 41 | 4.5 (1) | 23.8 (8) | 5.5 (1) | 28.9 (9) | 3/3 | 3/3 |
| 5 | Glypican-1 | P35052 | 62 | 14.6 (6) | 22.5 (9) | 0 | 0 | 3/3 | 0/3 |
| 6 | Melanotransferrin | P08582 | 80 | 0 | 13.6 (8) | 1 (1) | 6.3 (5) | 3/3 | 3/3 |
| 7 | Urokinase plasminogen activator surface receptor | Q03405 | 37 | 4.9 (1) | 19.7 (4) | 3.3 (1) | 16.6 (4) | 3/3 | 3/3 |
| 8 | CD59 glycoprotein | P13987 | 14 | 0 | 14.6 (2) | 12.0 (1) | 19.3 (3) | 2/3 | 3/3 |
| 9 | Carboxypeptidase M | P14384 | 51 | 0 | 5.2 (2) | 0 | 2.8 (1) | 2/3 | 1/3 |
| 10 | Glypican-5 | P78333 | 64 | 2.9 (1) | 3.5 (2) | 0 | 0 | 2/3 | 0/3 |
| 11 | 5'-Nucleotidase | P21589 | 63 | 0 | 3.7 (2) | 6.2 (2) | 7.9 (3) | 2/3 | 1/3 |
| 12 | Lymphocyte function-associated antigen 3 | P19256 | 28 | 0 | 2.4 (1) | 0 | 6.0 (2) | 1/3 | 2/3 |
| 13 | Cadherin-13 | P55290 | 78 | 0 | 4.2 (3) | 0 | 5.1 (3) | 3/3 | 3/3 |
| 14 | Mesothelin | Q13421 | 69 | 4.4 (3) | 6.4 (3) | 0 | 1.8 (1) | 3/3 | 1/3 |
| 15 | NKG2D ligand 3 | Q9BZM4 | 28 | 0 | 9.8 (2) | 0 | 0 | 3/3 | 0/3 |
| 16 | Growth arrest-specific protein 1 | P54826 | 36 | 0 | 7.3 (2) | 0 | 0 | 2/3 | 0/3 |
| 17 | Testisin | Q9Y6M0 | 35 | 0 | 5.6 (1) | 0 | 0 | 2/3 | 0/3 |
| 18 | NKG2D ligand 2 | Q9BZM5 | 27 | 2.7 (1) | 7.0 (2) | 0 | 2.4 (1) | 2/3 | 1/3 |
| 19 | Major prion protein | P04156 | 28 | 0 | 5.0 (1) | 0 | 0 | 2/3 | 0/3 |
| 20 | Ephrin-A1 | P20827 | 24 | 0 | 0 | 0 | 6.7 (1) | 0/3 | 2/3 |
| 21 | Reticulon-4 receptor-like 2 | Q86UN3 | 46 | 0 | 0 | 0 | 4.3 (2) | 0/3 | 2/3 |
| 22 | Ly6/PLAUR domain-containing protein 3 | O95274 | 36 | 0 | 0 | 2.0 (1) | 6.8 (2) | 0/3 | 2/3 |
| 23 | Reticulon-4 receptor | Q9BZR6 | 51 | 0 | 0 | 2.5 (1) | 4.9 (1) | 0/3 | 2/3 |
| 24 | Laminin subunit alpha-4c) | Q16363 | 203 | 12.1 (17) | 5.2 (7) | 0 | 0.5 (1) | 3/3 | 1/3 |
| 25 | Voltage-gated Ca2+ channel subunit α-2/δ-1d) | P54289 | 125 | 0 | 3.8 (4) | 0 | 3.1 (3) | 3/3 | 2/3 |
| 26 | Fibulin-1c) | P23142 | 77 | 9.7 (5) | 6.5 (3) | 3.9 (2) | 2.4 (1) | 3/3 | 1/3 |
| 27 | Fibulin-3c) | Q12805 | 55 | 7.1 (3) | 0 | 3.5 (1) | 4.6 (2) | 0/3 | 2/3 |
| 28 | Neuronal growth regulator 1 | Q7Z3B1 | 39 | 0 | 0 | 0 | 12.3 (3) | 0/3 | 3/3 |
| 29 | Glypican-4 | O75487 | 62 | 0 | 2.0 (1) | 0 | 0 | 1/3 | 0/3 |
| 30 | Ly6/PLAUR domain-containing protein 6B | Q8NI32 | 21 | 0 | 4.9 (1) | 0 | 0 | 1/3 | 0/3 |
| 31 | Hyaluronidase-2 | Q12891 | 54 | 0 | 0 | 0 | 2.3 (1) | 0/3 | 1/3 |
| 32 | Intercellular adhesion molecule 5c) | Q9UMF0 | 97 | 0 | 1.1 (1) | 0 | 0 | 1/3 | 0/3 |
| 33 | Deoxyribonuclease-1-like 1c) | P49184 | 34 | 0 | 3.9 (1) | 0 | 0 | 1/3 | 0/3 |
For each enrichment method, the average percent sequence coverage (Avg % Seq Cov) and average number of unique peptides (Avg Pep) across three biological replicates are indicated. The far right columns show the reproducibility of a protein identification using a given enrichment method (+PLC only) across three biological replicates. PLC, phospholipase C.
Theoretical molecular weight of precursor protein in kDa.
The minimum number of unique peptides required for a protein identification was 2, but due to averaging across triplicate samples, the average peptides may appear to be 1. A complete listing of the number of peptides for each replicate can be found in Supporting Information Table 5 and all peptides used in identifications are listed in Supporting Information Table 6.
Peptides match specific isoforms predicted to contain a GPI anchor though other isoforms cannot be excluded.
Experimentally proven to be GPI anchored in other studies but not annotated as a GPI-AP in the UniProt database.