MALDI MS peptide mapping performance by in-gel digestion on a probe with prestructured sample supports.
Matrix-assisted laser desorption/ionization (tandem) mass spectrometry (MALDI MS) is widely used in protein chemistry and proteomics research for the identification and characterization of proteins isolated by polyacrylamide gel electrophoresis. In an effort to minimize sample handling and increase sample throughput, we have developed a novel in-gel digestion protocol where sample preparation is performed directly on a MALDI probe with prestructured sample support. The protocol consists of few sample-handling steps and has minimal consumption of reagents, making the protocol sensitive, timesaving, and cost-efficient. Performance of the on-probe sample preparation protocol was demonstrated by analysis of a set of rat liver proteins obtained from a fluorescently stained (Cy3 and SyproRuby) two-dimensional polyacrylamide gel. The success rate of protein identification by on-probe tryptic digestion and MALDI peptide mass mapping was 89%. The on-probe in-gel digestion procedure provided superior sensitivity and peptide mass mapping performance as compared to our standard in-gel digestion protocol. The on-probe digestion technique resulted in significantly improved amino acid sequence coverage of proteins, mainly due to efficient recovery and detection of large (>1.5 kDa) hydrophobic peptides. These observations indicate that numerous tryptic peptides are lost when using the standard in-gel digestion methods and sample preparation techniques for MALDI MS. This study also demonstrates that the on-probe digestion protocol combined with MALDI tandem mass spectrometry provides a robust platform for proteomics research, including protein identification and determination of posttranslational modifications.
Klenø
Tina Guldberg
TG
Applied Trinomics, Novo Nordisk A/S, Måløv, Denmark.
Andreasen
Christian Maaløv
CM
Kjeldal
Helle Ørsted
HØ
Leonardsen
Lise Rønnedal
LR
Krogh
Thomas Nylandsted
TN
Nielsen
Per Franklin
PF
Sørensen
Marianne Vind
MV
Jensen
Ole Nørregaard
ON
D000818:Animals; D002417:Cattle; D015180:Electrophoresis, Gel, Two-Dimensional; D005782:Gels / Q000737:chemistry; D008099:Liver / Q000737:chemistry; D015335:Molecular Probes; D010449:Peptide Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry; D051381:Rats; D012680:Sensitivity and Specificity; D012710:Serum Albumin, Bovine / Q000737:chemistry; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000295:instrumentation / Q000379:methods*
D005782:Gels; D015335:Molecular Probes; D011506:Proteins; D012710:Serum Albumin, Bovine