Table I Statistics of the triplicate analysis of unfractionated HeLa digest using 2 h-gradient LC-MS/MS
Experiment 1Experiment 2Experiment 3
Full MS (Survey) Scans117691213612080
Chromatographic Features766037937281953
    Overlappinga70420 (91.9%)72933 (91.9%)75327 (91.9%)
    Identified (-)d26948 (35.2%)28539 (36.0%)27742 (33.9%)
    Identified (+)e34337 (44.8%)35937 (45.3%)34861 (42.5%)
MS/MS Scans533435397753940
    LysH+ and ArgH+b52297 (98.0%)53080 (98.3%)53017 (98.3%)
MS/MS Spectral Clones134031136143136396
    Multiplexing Rate (x)2.512.522.53
Peptide-spectrum Matchesc660426873465420
    Success Rate49%50%48%
    Identification Efficiency124%128%121%
Unique Peptide Sequences330663426132412
Protein Groups472647594682
  • a Overlapping was estimated in the RT-m/z space, where RT corresponds to feature's chromatographic trace (eluting peak width), and m/z equals to the MS/MS isolation width (±2.0 Th around the monoisotopic peak).

  • b Protonated lysine and arginine occurrences are calculated based on the co-existence of both peaks at m/z 147.11280 and 175.11895 in the MS/MS peak list, with 10 ppm tolerance.

  • c PSM list of unique peptide sequences was trimmed to 1.0% FDR.

  • d (-) Identified features without MS/MS cloning.

  • e (+) Identified features with MS/MS cloning allowed.