Ponomarenko Elena, Kopylov Arthur, Lisitsa Andrey, Radko Sergey, Kiseleva Yana, Kurbatov Leonid, Ptitsyn Konstantin, Tikhonova Olga, Moisa Alexander, Novikova Svetlana, Poverennaya Ekaterina, Ilgisonis Ekaterina, Filimonov Aleksey, Bogolubova Nadezhda, Averchuk Valentina, Karalkin Pavel, Vakhrushev Igor, Yarygin Konstantin, Moshkovskii Sergei, Zgoda Victor, Sokolov Alexey, Mazur Alexander, Prokhortchouck Egor, Skryabin Konstantin, Ilina Elena, Kostrjukova Elena, Alexeev Dmitry, Tyakht Alexander, Gorbachev Alexey, Govorun Vadim, Archakov Alexander
Peptide candidate signals were extracted by processing MassHunter raw data files with the in-house software system srm2prot that generates MS Excel reports for each acquired transition groups and the catalog of all the accepted candidates. Manual inspection was not carried out. No automatic comparison of the peptide candidate signals with the corresponding synthetic standards was carried out because of temporary limitations of srm2prot and acquired SRM data. Instead of comparing endogenous peptides with synthetic standards, the scheduled SRM acquisition methods with narrow time window were built and used to acquire SRM data.
MS Excel reports provide navigation through accepted peptide candidate signals only if srm2prot.xla AddIn is installed. To install srm2prot.xla MS Excel AddIn in 3 clicks use the installation package srm2prot_xla.exe.
srm2prot MS Excel peptide report contains:
|Pivot table of peptide candidate signals:||jpr2013-bio-stat.xlsx||119 KB||MS Excel 2007||Stats on acquired, detected, success rate, observed signals for each peptide grouped by HepG2 and HPL.|
|Catalog of the found and accepted peptide candidate signals:||jpr2013-bio.xlsx||4.1 MB||MS Excel 2007/srm2prot||249 proteins (100%), 451 peptides (96%), 22 847 candidate signals|
|Assay:||assay catalog||3 files||Original and specialized for MassHunter, mMap3 and PASSEL||2055 transitions of 467 peptides of 249 proteins in 16 scheduled MRM methods|
|Acquired SRM data files:||Raw SRM data catalog||3.59 GB||Agilent Triple Quadrupole LC-MS/MS 6490, MassHunter 6.0||440 files acquired on HepG2 cells and depleted plasma samples|
|srm2prot reports separately:||jpr2013-bio reports||488* KB||MS Excel 2007, srm2prot.xla AddIn||6 GB in total, min 167 KB, max 2.78 MB; 468 directories* with 12 948 report files in total|
|srm2prot reports archived into one big file:||jpr2013-bio-reports.exe||5.1 GB||7z, LZMA, self-extracting||Archived MS Excel documents into one self-extracting package|
|Processing SRM data:||event log||2 MB||Time for searching for candidates by srm2prot: 48 min.||MS Excel reports generation: 15h 50m|
|Archived SRM data deposited into PASSEL (Institute for Systems Biology):||PASS00278||531 MB||Protocols: extraction, separation, digestion, acquisition.||Assay and 31 zipped raw SRM data files.|
See also the previous article.
The reports have been developed and prepared by Aleksey Filimonov for IBMC n. Orekhovich and the article in 2013.