Technique Application Protein Pattern Identification (protein/sample) Quantification (protein/sample) throughput (sample / day) Information Ease of use Cost effectiveness Biomarker discovery Clinical Diagnosis SELDI-MS Proteins, peptides +++ - - >1000 + +++ ++ +++ MALDI-MS Proteins, peptides +++ - - >1000 ++ +++ ++ +++ LC-MS Proteins, peptides ++ - - >20 +++ ++ + ++ MALDI-MS/MS Proteins, peptides - >10 - >100 ++ ++ ++ ++ LC-MS/MS Proteins, peptides, metabolites - >100 >100 >10 +++ ++ +++ + 2D-LC-MS/MS (MudPIT) Proteins, peptides, metabolites - >1000 >500 <1 +++ + +++ + 1D-GE – MALDI-MS(/MS) Proteins, peptides - <100 <100 <1 +++ ++ +++ + 1D-GE – LC-MS/MS Proteins, peptides - >100 >100 <1 +++ ++ +++ + 2D-GE – MALDI-MS(/MS) Proteins, peptides - >200 >200 <1 +++ + +++ + LC-MS/MS (MRM) Proteins, peptides - - >100 >20 + + + + MALDI-MSI Proteins, peptides, metabolites ++ - - <10 + + ++ +++ SPR(-MS) DNA, RNA, proteins, metabolites - + ++ >10 +++ ++ ++ +

Table 3: Throughput, usefulness and cost effectiveness of various MS-based proteomic platforms for biomarker discovery and clinical diagnosis of cancer.