Table 1

Protein fractionation, peptide separation and mass spectrometric identification strategies for enhancement of proteome identification coverage explored in this study.

Steps

Procedures


(A) Protein fractionation

(1) SDS-PAGE slicing

(2) Serial ultrafiltration

(3) No protein fractionation

(B) Tryptic digestion

(1) In-solution digestion

(2) In-gel digestion

(C) Peptide chromatography

(1) Strong cation exchange chromatograhpy

(2) Strong anion exchange chromatograhpy

(3) C18 ion pair chromatograhpy

(4) PSDVB with NH4OH, using StageTip

(5) No peptide chromatography

(D) Parent ion selection in LC-MS

(1) Simple repetition

(2) Sequential static exclusion

(3) Different ion pair reagents in subsequent runs

(4) Subdivided scan range

(5) Shallow gradient elution

(E) CID for MS/MS

(1) Quadrupole-TOF

(2) Linear ion trap


Abbreviations: SDS-PAGE, sodium dodecylsulfate polyacrylamide gel electrophoresis; PSDVB, poly(styrene-divinylbenzene) copolymer; TOF: time-of-flight.

Ishihama et al. BMC Genomics 2008 9:102   doi:10.1186/1471-2164-9-102

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