1. Experiment was performed on 293 cells, details are presented in publication: Adenoviral E4 gene stimulates secretion of PEDF that maintains long-term survival of human glomerulus-derived endothelial cells Marina Jerebtsova‡§*, Namita Kumari‖, Yuri Obuhkov‖, and Sergei Nekhai‖†* (to be published in Molecular and Cellular Proteomics), please see more details in paper

2. Sample: 293 cells conditioned by E4 – Raw Excalibur spectra files represented by files MJ_1_9.raw,..MJ_1_16.raw – Proteome Discovere 1.2 SEQUEST search files represented by MJ_1_9.msf,.., MJ_1_16.msf Control: 293 cells – Raw Excalibur spectra files represented by files SN_2_9.raw,..SN_1_18.raw – Proteome Discovere 1.2 SEQUEST search files represented by SN_2_9.msf,.., SN_2_18.msf SEQUEST search was made on human.fasta database. Each file corresponds to gel band and set of files represent two samples MJ and SN respectively

3. Procedure and tests Workflow ₋ HPLC on PicoFrit C18 column, gradient 60 min from 2% to 30% ACN ₋ Nanospray 2 kV, flow rate 300 nL/min ₋LTQ Orbitrap MS. Data dependent scan FT MS + 3 FT MS/MS. A blank water run was performed after each sample run Each 24 hours setup performance was tested on Apomyoglobin sample, 12 fmol. Coverage was 39-79 % Search is made by SEQUEST on human database