Mass spectrometry has become the technology of choice for detailed identification of proteins in complex mixtures. Although electrophoretic separation, proteolytic digestion, mass spectrometric analysis of unseparated digests, and database searching have become standard methods in widespread use, peptide sequence information obtained by collision-induced dissociation and tandem mass spectrometr...

A metabolite of cyclosporine has been isolated and its structure identified through use of HPLC and tandem mass spectroscopy. Fast atom bombardment mass spectrometry of an HPLC fraction co-eluting with 1 eta hydroxy-cyclosporine (M17) indicated that the mass of this metabolite was 2 Da greater than that of cyclosporine. Further isolation by HPLC yielded a pure fraction, which we analyzed with t...

Tandem mass spectrometry is a widely used method for protein and peptide sequences identification. Since the mass spectra contain up to 80% of noise and many other inaccuracies, there still exists a need for more accurate algorithms for mass spectra interpretation. The sizes of protein databases grow rapidly and the methods for indexing these databases in order to interpret mass spectra become ...

Tandem mass spectrometry is a widely used method for protein and peptide sequences identification. Since the mass spectra contain up to 80% of noise and many other inaccuracies, there still exists a need for more accurate algorithms for mass spectra interpretation. The sizes of protein databases grow rapidly and the methods for indexing these databases in order to interpret mass spectra become ...

conclusions cd5l might be a useful biomarker for early diagnosis of hcc in hcv cirrhotic patients. lrg and hp α2 isoforms could be potential markers for distinguishing viral hcc. our results also further support the presence of varying molecules involved in hepatocarcinogenesis in hbv when compared with hcv infection. patients and methods two-dimensional polyacrylamide gel electrophoresis combi...

High-performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry was used to identify flavone aglycones and glycosides in soybean pods. Tandem mass spectrometry (MS-MS and MS-MS-MS) and photodiode array detection were also utilized in flavone characterization. A total of seven flavone aglycones and glycosides were identified. Among them three flavone aglycones--...

Database-searching algorithms compatible with shotgun proteomics match a peptide tandem mass spectrum to a predicted mass spectrum for an amino acid sequence within a database. SEQUEST is one of the most common software algorithms used for the analysis of peptide tandem mass spectra by using a cross-correlation (XCorr) scoring routine to match tandem mass spectra to model spectra derived from p...

A novel methodology for the de novo identification of peptides by mixed-integer optimization and tandem mass spectrometry is presented in this article. The various features of the mathematical model are presented and examples are used to illustrate the key concepts of the proposed approach. Several problems are examined to illustrate the proposed method's ability to address (1) residue-dependen...

Tandem mass spectrometry has emerged to be one of the most powerful high-throughput techniques for protein identification. Tandem mass spectrometry selects and fragments peptides of interest into N-terminal ions and C-terminal ions, and it measures the mass/charge ratios of these ions. The de novo peptide sequencing problem is to derive the peptide sequences from given tandem mass spectral data...

In this study, we present a preprocessing method for quadrupole time-of-flight (Q-TOF) tandem mass spectra to increase the accuracy of database searching for peptide (protein) identification. Based on the natural isotopic information inherent in tandem mass spectra, we construct a decision tree after feature selection to classify the noise and ion peaks in tandem spectra. Furthermore, we recogn...