Nature Methods
2, 667 - 675 (2005)
Published online: 23 August 2005; | doi:10.1038/nmeth785
Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigationsJoshua E Elias, Wilhelm Haas, Brendan K Faherty
& Steven P Gygi Supplementary Fig. 1 (pdf 3M)
Mascot and SEQUEST score distributions for target (blue) and decoy (red) database hits. Supplementary Fig. 2 (pdf 108K)
Examples of MS/MS acquired by LTQ or QSTAR mass spectrometers. Supplementary Fig. 3 (pdf 916K)
Representation of MS/MS quality on LTQ and QSTAR and its influence on Mascot and SEQUEST scoring. Supplementary Fig. 4 (pdf 76K)
Comparison of LTQ and QSTAR acquisitions from equal gradient analyses. Supplementary Fig. 5 (pdf 84K)
Proteins identified by just one instrument appear to be less abundant than those identified by both LTQ and QSTAR. Supplementary Fig. 6 (pdf 316K)
Differential preference for ions selected for MS/MS by LTQ and QSTAR mass spectrometers influences the length distribution of identified peptides. Supplementary Table 1 (pdf 64K)
Mascot and SEQUEST score filter criteria applied to MS/MS spectra acquired on the LTQ and QSTAR mass spectrometers to achieve ~99% precision (1% false positive rate) at maximum estimated sensitivity. Supplementary Methods (pdf 84K) Supplementary Data (pdf 109K) Supplementary Discussion (pdf 112K)
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