Increased Protein Identification Capabilities Through Novel Tandem MS Calibration Strategies
High mass measurement accuracy is critical for confident protein identification and characterization in proteomics research. Fourier transform ion cyclotron resonance (FTICR) mass spectrometry is a unique technique which can provide unparalleled mass accuracy and resolving power. However, the mass measurement accuracy of FTICR-MS can be affected by space charge effects. Here we present a novel internal calibrant-free calibration method that corrects for space charge-induced frequency shifts in FTICR fragment spectra called Calibration Optimization on Fragment Ions (COFI). This new strategy utilizes the information from fixed mass differences between two neighboring peptide fragment ions (such as y1 and y2) to correct the frequency shift after data ollection. COFI has been successfully applied to LC-FTICR fragmentation data. Mascot MS/MS ion search data demonstrate that most of the fragments from BSA tryptic digested peptides can be identified using a much lower mass tolerance window after applying COFI to LC-FTICR-MS/MS of BSA tryptic digest. Furthermore, COFI has been used for multiplexed LC-CID-FTICR-MS which is an attractive technique because of its increased duty cycle and dynamic range. After the application of COFI to a multiplexed LC-CID-FTICR-MS of BSA tryptic digest, we achieved an average measured mass accuracy of 2.49 ppm for all the identified BSA fragments.
- Research Organization:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- AC05-76RL01830
- OSTI ID:
- 913610
- Report Number(s):
- PNNL-SA-45955; 17791; KP1102010; TRN: US200802%%897
- Journal Information:
- Journal of Proteome Research, 4(4):1434-1441, Vol. 4, Issue 4
- Country of Publication:
- United States
- Language:
- English
Similar Records
Estimating Probabilities of Peptide Database Identifications to LC-FTICR-MS Observations
Identification of Tryptic Peptides from Large Databases using Multiplexed Tandem Mass Spectrometry: Simulations and Experimental Results