SRM data and reports for

Chromosome 18 TranscriptoProteome of Liver Tissue and HepG2 Cells and Targeted Proteome Mapping in Depleted Plasma: Update 2013, J. of Proteome Res.

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.xlsx119 KBMS 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.xlsx4.1 MBMS Excel 2007/srm2prot249 proteins (100%), 451 peptides (96%), 22 847 candidate signals
Assay:assay catalog3 files Original and specialized for MassHunter, mMap3 and PASSEL2055 transitions of 467 peptides of 249 proteins in 16 scheduled MRM methods
Acquired SRM data files:Raw SRM data catalog3.59 GB Agilent Triple Quadrupole LC-MS/MS 6490, MassHunter 6.0440 files acquired on HepG2 cells and depleted plasma samples
srm2prot reports separately:jpr2013-bio reports488* KB MS Excel 2007, srm2prot.xla AddIn6 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.exe5.1 GB 7z, LZMA, self-extractingArchived MS Excel documents into one self-extracting package
Processing SRM data:event log2 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):PASS00278531 MBProtocols: 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.