Utilization of high-accuracy FTICR-MS data in protein quantitation experiments.
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.
Strohalm
Martin
M
Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague, 142 20, Czech Republic.
Novak
Petr
P
Pompach
Petr
P
Man
Petr
P
Kavan
Daniel
D
Witt
Matthias
M
Dzubak
Petr
P
Hajduch
Marian
M
Havlicek
Vladimir
V
D018929:Cell Culture Techniques; D045744:Cell Line, Tumor; D002945:Cisplatin; D003470:Culture Media / Q000378:metabolism; D006801:Humans; D007553:Isotope Labeling / Q000379:methods; D013058:Mass Spectrometry / Q000379:methods*; D011506:Proteins / Q000032:analysis* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods*
D003470:Culture Media; D011506:Proteins; D002945:Cisplatin