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Identification and quantification of peptides and proteins secreted from prostate epithelial cells by unbiased liquid chromatography tandem mass spectrometry using goodness of fit and analysis of variance
- Source :
- Journal of proteomics. 75(4)
- Publication Year :
- 2011
-
Abstract
- The proteins secreted by prostate cancer cells (PC3(AR)6) were separated by strong anion exchange chromatography, digested with trypsin and analyzed by unbiased liquid chromatography tandem mass spectrometry with an ion trap. The spectra were matched to peptides within proteins using a goodness of fit algorithm that showed a low false positive rate. The parent ions for MS/MS were randomly and independently sampled from a log-normal population and therefore could be analyzed by ANOVA. Normal distribution analysis confirmed that the parent and fragment ion intensity distributions were sampled over 99.9% of their range that was above the background noise. Arranging the ion intensity data with the identified peptide and protein sequences in structured query language (SQL) permitted the quantification of ion intensity across treatments, proteins and peptides. The intensity of 101,905 fragment ions from 1421 peptide precursors of 583 peptides from 233 proteins separated over 11 sample treatments were computed together in one ANOVA model using the statistical analysis system (SAS) prior to Tukey–Kramer honestly significant difference (HSD) testing. Thus complex mixtures of proteins were identified and quantified with a high degree of confidence using an ion trap without isotopic labels, multivariate analysis or comparing chromatographic retention times.
- Subjects :
- Male
Population
Biophysics
Peptide
Biochemistry
High-performance liquid chromatography
Ion
Liquid chromatography–mass spectrometry
Tandem Mass Spectrometry
medicine
Humans
False Positive Reactions
education
chemistry.chemical_classification
Ions
education.field_of_study
Analysis of Variance
Chromatography
Models, Statistical
Chemistry
Prostate
Reproducibility of Results
Epithelial Cells
Trypsin
Secretory protein
14-3-3 Proteins
Ion trap
Peptides
Algorithms
Software
medicine.drug
Chromatography, Liquid
Subjects
Details
- ISSN :
- 18767737
- Volume :
- 75
- Issue :
- 4
- Database :
- OpenAIRE
- Journal :
- Journal of proteomics
- Accession number :
- edsair.doi.dedup.....e396aacddb874377dbbe33295d40482e