Immunoproteomics using polyclonal antibodies and stable isotope-labeled affinity-purified recombinant proteins.
The combination of immuno-based methods and mass spectrometry detection has great potential in the field of quantitative proteomics. Here, we describe a new method (immuno-SILAC) for the absolute quantification of proteins in complex samples based on polyclonal antibodies and stable isotope-labeled recombinant protein fragments to allow affinity enrichment prior to mass spectrometry analysis and accurate quantification. We took advantage of the antibody resources publicly available from the Human Protein Atlas project covering more than 80% of all human protein-coding genes. Epitope mapping revealed that a majority of the polyclonal antibodies recognized multiple linear epitopes, and based on these results, a semi-automated method was developed for peptide enrichment using polyclonal antibodies immobilized on protein A-coated magnetic beads. A protocol based on the simultaneous multiplex capture of more than 40 protein targets showed that approximately half of the antibodies enriched at least one functional peptide detected in the subsequent mass spectrometry analysis. The approach was further developed to also generate quantitative data via the addition of heavy isotope-labeled recombinant protein fragment standards prior to trypsin digestion. Here, we show that we were able to use small amounts of antibodies (50 ng per target) in this manner for efficient multiplex analysis of quantitative levels of proteins in a human HeLa cell lysate. The results suggest that polyclonal antibodies generated via immunization of recombinant protein fragments could be used for the enrichment of target peptides to allow for rapid mass spectrometry analysis taking advantage of a substantial reduction in sample complexity. The possibility of building up a proteome-wide resource for immuno-SILAC assays based on publicly available antibody resources is discussed.
From the ‡Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden;
Fredrik
F
Edfors
¶Department of Proteomics, KTH - Royal Institute of Technology, SE-106 91 Stockholm, Sweden;
Tove
T
Boström
From the ‡Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden;
Björn
B
Forsström
‖Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany;
Marlis
M
Zeiler
**Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, SE-171 21 Stockholm, Sweden.
Henrik
H
Johansson
From the ‡Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden;
Emma
E
Lundberg
¶Department of Proteomics, KTH - Royal Institute of Technology, SE-106 91 Stockholm, Sweden;
Sophia
S
Hober
**Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, SE-171 21 Stockholm, Sweden.
Janne
J
Lehtiö
‖Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany;
Matthias
M
Mann
From the ‡Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden; ¶Department of Proteomics, KTH - Royal Institute of Technology, SE-106 91 Stockholm, Sweden;
Mathias
M
Uhlen
D000906:Antibodies / Q000276:immunology; D002853:Chromatography, Liquid; D000939:Epitopes / Q000096:biosynthesis / Q000302:isolation & purification; D015972:Gene Expression Regulation, Neoplastic; D006367:HeLa Cells; D006801:Humans; D007553:Isotope Labeling; D013058:Mass Spectrometry; D009363:Neoplasm Proteins / Q000096:biosynthesis*; D040901:Proteomics / Q000379:methods*; D011994:Recombinant Proteins / Q000096:biosynthesis* / Q000276:immunology / Q000302:isolation & purification
D000906:Antibodies; D000939:Epitopes; D009363:Neoplasm Proteins; D011994:Recombinant Proteins