Table. 1.

Methodologies to study cell secretomes with their potential advantages and disadvantages.

Methodologies	Advantages	Disadvantages
SAGE	Direct, quantitative method Genome knowledge not required	Low-throughput, time consuming Same tag on multiple gene Sequencing error, quantitation bias Low abundance transcript missed
DNA microarray	High-throughput, quantitativemethod	Knowledge of sequences required Rare transcripts missed Labeling and hybridization biases Identify differentially expressedgenes only.
Antibody and bead arrays	Sensitive and specific method Low abundance transcriptdetected Reproducible	Expensive Availability of specific antibody Non-specific binding Fast denaturation of proteins
Mass spectrometry 2-DE DIGE ICAT iTRAQ SILAC SELDI-TOF	High resolving power Low abundance transcript detected only with ICAT, iTRAQand SILAC Good sequence coverage	Rare transcripts not detected with2-DE and DIGE Limited reproducibility with 2-DE andDIGE ICAT only applicable to cysteinecontaining proteins Limited dynamic range SILAC not applicable to clinicalproteins in vivo
RNA sequencing	Genome knowledge not required Non-model organisms can beused	Large amount of data, storage Bioinformatics challenge Only structural/sequence information Rare transcripts missed Strand biases Amplification selection andhybridization artifacts
Yeast Secretion Trap (YST)	Functional method Sequence information alsoobtained	Mammalian proteins not working inyeast Low abundance proteins missed Proteins lacking signal peptidemissed
Computation algorithms	Predict secretory proteins	Not based on experimental data mRNA levels may not correlate withprotein levels