Table III

Peptides, observed transitions, and average limits of detection for peptides detected via AIMS by MRM-based methods

“Attempted” transitions were derived from the Orbitrap linear ion trap MS/MS spectra, and “observed” transitions were the number actually seen on the 4000 Q Trap. The average (Avg) peptide limit of detection (LOD) was computed by adding the individual peptide limits of detection for each protein and dividing by the total number of peptides observed for that protein.

Small scale experiment
Protein nameNumber of peptides detectedTotal transitions observed vs. attempted at 100a or 66b ng/mlTotal transitions observed vs. attempted at 10a or 33b ng/mlAvg peptide LOD
ng/ml
AKRF1C1a28/118/1133
BHMTb524/2924/2910
Calreticulin precursora210/1310/1310
PP1Gb629/3625/3633
Large scale experiment
Protein nameNumber of peptides detectedTotal transitions observed vs. attempted at 100 ng/mlTotal transitions observed vs. attempted at 10 ng/mlAvg peptide LOD
ng/ml
ADP-ribosylation factor 616/66/610
AKRF1C1419/2411/2432.5
AKRF1C228/122/1255
PDZ and LIM domain 1 (elfin)311/154/1540
S100 calcium-binding protein A129/116/1110
S100 calcium-binding protein, β315/1514/1510
Annexin I525/3014/3046
Annexin IV29/129/1210
Brain creatine kinase312/158/1540
Calreticulin precursor313/202/2040
Chromogranin A precursor523/3016/3028
Cystatin B16/65/610
Enolase 2310/172/1770
Fibroblast growth factor 1 (acidic) isoform 1 precursor15/53/510
Fructose-bisphosphate aldolase C29/121/1255
Glucose-phosphate isomerase628/3627/3610
Glutathione S-transferase M1 isoform 115/51/510
Glutathione S-transferase M215/65/610
Glutathione S-transferase M3313/1610/1640
Growth arrest and DNA damage-inducible, γ211/1111/1110
Heat shock 27-kDa protein 1419/238/2355
Inhibitor of DNA binding 215/54/510
Interleukin 18 proprotein14/54/510
Non-metastatic cells 1, protein (NM23A) isoform b312/1612/1610
Peroxiredoxin 2 isoform a210/117/1110
Phosphoserine aminotransferase isoform 1315/1613/1610
Ser (or Cys) proteinase inhibitor, clade B, member 314/50/5100
Spermidine/spermine N1-acetyltransferase28/115/1155
Superoxide dismutase 1, soluble210/106/1010
Transgelin13/52/510
Tyr 3-/Trp 5-monooxygenase activation protein, ε421/2116/2110
Ubiquitin-conjugating enzyme E2C isoform 2210/1010/1010
Ubiquitin-conjugating enzyme E2I423/2420/2410
Ubiquitin-conjugating enzyme E2N628/3127/3110