Table 1.
Protein identification results from Saccharomyces cerevisiae datasets. Column 1 refers to the number of MS/MS spectra that were matched to a peptide below a 1% false-discovery rate, as estimated by Percolator. Column 2 lists the number of protein identifications for each instrument/method, along with a false-discovery rate at the protein level, estimated by a reverse-database strategy. Column 3 lists the percentage of all identified proteins found by a particular instrument/method combination. The group of columns marked “Percent overlap” lists percent of proteins in instrument/method row found by instrument/method column. For example, 74.3% of the proteins found in Velos DDA were also found in LTQ DDA.
| Number of matched MS/MS spectra |
Number of proteins identified; protein FDR (Total = 3335) |
Percentage of all identified proteins |
Percent overlap | ||||||
|---|---|---|---|---|---|---|---|---|---|
| LTQ DDA |
IF- LTQ DDA |
Velos DDA |
LTQ DIA |
IF- LTQ DIA |
Velos DIA |
||||
| LTQ DDA |
74900 | 1791; 6.6% |
53.7 | 77.2 | 78.7 | 81.3 | 83.8 | 81.8 | |
| IF-LTQ DDA |
92246 | 1783; 8.2% |
53.5 | 77.1 | 78.8 | 81.0 | 84.2 | 81.3 | |
| Velos DDA |
142135 | 1895; 11.7% |
56.8 | 74.3 | 74.5 | 77.4 | 80.7 | 78.2 | |
| LTQ DIA |
20028 | 2094; 3.2% |
62.8 | 69.0 | 68.9 | 69.7 | 86.7 | 79.8 | |
| IF-LTQ DIA |
25600 | 2321; 3.5% |
69.6 | 64.2 | 64.6 | 65.6 | 78.3 | 79.4 | |
| Velos DIA |
33913 | 2146; 4.3% |
64.3 | 68.1 | 67.8 | 69.1 | 78.2 | 86.2 | |