Amine specific peptide reactive group (NHS)

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Amine specific peptide reactive group (NHS) Quantitation by iTRAQ and TMT Balance group mass 31-28 (neutral loss) 13C 18O (+3) 18O (+2) 13C (+1) (+0) Amine specific peptide reactive group (NHS) Reporter group mass 114-117 (retains charge) m/z 114 (+1) 13C m/z 115 (+2) 13C2 m/z 116 (+3) 13C2 15N m/z 117 (+4) 13C3 15N Isobaric tag Total mass 144

iTRAQ 8-plex

Tandem Mass Tags (TMT)

Participants Laboratory Instrument Search Engine CIMA QTOFµ Masot CIPF QSTAR ProteinPilot CNB MALDI TOFTOF 4800 Phenyx ICS INIBIC LP-CSICUAB LTQ Sequest PCB MALDI TOFTOF 4700 Orbitrap CMU (TMT) (R1, R2, offgel) R2 Quixote UCM-PCM UCO (2) UPF 18 Data sets

Results Not all protein data was submitted in the excel files. The total number of unique peptide sequences within each data set are 19207. Of these sequences 9468 are unique in all the data sets. # of peptides Only 3 peptides found in 15 data sets: 1 from CYC, 1 from MYG and the other from Ecoli. Data sets

Results

Results

Results

Results MALDI TOFTOF Q TOF Orbitrap LTQ TMT # of peptides Data Set

Results

Results Ratio A/B Data Set Mascot Phenyx ProteinPilot Sequest TMT Quixote Ratio A/B Data Set

Results MALDI TOFTOF Q TOF Orbitrap LTQ TMT Ratio A/B Data Set