Utilization of high-accuracy FTICR-MS data in protein quantitation experiments

• Published in: Journal of mass spectrometry. Vol. 44; no. 11; pp. 1565 - 1570
• Main Authors: Strohalm, Martin, Novak, Petr, Pompach, Petr, Man, Petr, Kavan, Daniel, Witt, Matthias, Dzubak, Petr, Hajduch, Marian, Havlicek, Vladimir
• Format: Journal Article
• Language: English
• Published: Chichester, UK John Wiley & Sons, Ltd 01.11.2009; Wiley
• Subjects: Amino acids; Analytical, structural and metabolic biochemistry; Biological and medical sciences; Cell Culture Techniques; Cell Line, Tumor; Cisplatin; Culture; Culture Media - metabolism; Data processing; Fingerprinting; Fundamental and applied biological sciences. Psychology; General aspects, investigation methods; Humans; Isotope Labeling - methods; Mass spectrometry; Mass Spectrometry - methods; protein quantitation; Proteins; Proteins - analysis; Proteins - metabolism; Proteomics - methods; Reproducibility of Results; SILAC; Software; Spectroscopy, Fourier Transform Infrared - methods; Strategy; Tolerances; workflow; Antineoplastic agent; Tandem mass spectrometry; Fourier transformation; Chemical analysis; Isotope labelling; Peptides; protein quantitation; software; Leukemia; HPLC chromatography; Matrix assisted laser desorption ionization; Electrospray; Posttranslational modification; Qualitative analysis; Tumor cell; Quantitative analysis; Human; workflow; Coupled method; Ion cyclotron resonance spectrometry; SILAC; Cisplatin; Protein; Stable isotope labeling by amino acids in cell culture; Reversed phase chromatography; Cell line; Analysis method; Peptide fragment; Time of flight method; Proteomics; Measurement accuracy; Mass spectrometry
• ISSN: 1076-5174; 1096-9888; 1096-9888
• DOI: 10.1002/jms.1602

Human acute T-lymphoblastic leukemia cell line (CEM) treated with cisplatin, and the stable isotope labeling by amino acids in cell culture (SILAC) strategy were used to present an improved method of data processing in high-accuracy mass spectrometry (MS). By using peptide mass fingerprinting with low mass tolerance, we were able to utilize far more data retained in MS scans which would normally be missed by a standard processing method. This new way of data interpretation results in an improvement of the relevance of quantitation experiments and enabled us to search and quantify different types of posttranslational modifications. Furthermore, we used this technique to distinguish among different protein isoforms, commonly returned by Mascot search engine. Copyright © 2009 John Wiley & Sons, Ltd.