Automated selected reaction monitoring software for accurate label-free protein quantification.
Selected reaction monitoring (SRM) is a mass spectrometry method with documented ability to quantify proteins accurately and reproducibly using labeled reference peptides. However, the use of labeled reference peptides becomes impractical if large numbers of peptides are targeted and when high flexibility is desired when selecting peptides. We have developed a label-free quantitative SRM workflow that relies on a new automated algorithm, Anubis, for accurate peak detection. Anubis efficiently removes interfering signals from contaminating peptides to estimate the true signal of the targeted peptides. We evaluated the algorithm on a published multisite data set and achieved results in line with manual data analysis. In complex peptide mixtures from whole proteome digests of Streptococcus pyogenes we achieved a technical variability across the entire proteome abundance range of 6.5-19.2%, which was considerably below the total variation across biological samples. Our results show that the label-free SRM workflow with automated data analysis is feasible for large-scale biological studies, opening up new possibilities for quantitative proteomics and systems biology.
Protein Technology, Department of Immunotechnology, Lund University, BMC D13, 22184 Lund, Sweden.
Johan
J
Teleman
Christofer
C
Karlsson
Sofia
S
Waldemarson
Karin
K
Hansson
Peter
P
James
Johan
J
Malmström
Fredrik
F
Levander
D000222:Adaptation, Physiological; D000465:Algorithms; D001426:Bacterial Proteins / Q000378:metabolism*; D053898:Biosynthetic Pathways; D003470:Culture Media; D005227:Fatty Acids / Q000096:biosynthesis; D006801:Humans; D013058:Mass Spectrometry / Q000592:standards; D010449:Peptide Mapping / Q000379:methods / Q000592:standards; D010949:Plasma; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics; D012015:Reference Standards; D012984:Software; D018709:Statistics, Nonparametric; D013297:Streptococcus pyogenes / Q000254:growth & development / Q000378:metabolism / Q000502:physiology
D001426:Bacterial Proteins; D003470:Culture Media; D005227:Fatty Acids; D020543:Proteome