Chromosome 18 Transcriptome Profiling and Targeted Proteome Mapping in Depleted Plasma, Liver Tissue and HepG2 Cells. J. Proteome Res.

Zgoda Victor, Kopylov Arthur, Tikhonova Olga, Moisa Alexander, Novikova Svetlana, Pyndyk Nadezda, Farafonova Tatyana, Lisitsa Andrey, Ponomarenko Elena, Poverennaya Ekaterina, Radko Sergey, Khmeleva Svetlana, Kurbatov Leonid, Filimonov Aleksey, Bogolyubova Nadezda, Ilgisonis Ekaterina, Chernobrovkin Aleksey, Ivanov Alexis, Medvedev Alexei, Mezentsev Yury, Moshkovskii Sergei, Naryzhny Stanislav, Ilina Elena, Kostrjukova Elena, Alexeev Dmitry, Tyakht Alexander, Govorun Vadim, Archakov Alexander

SRM data, protocols, reports and summaries of measurements

Candidate peak groups were extracted by processing MassHunter raw data files with in-house specially extended version of mQuest/mProphet that generates ms2prot reports to automate peptide detection. Manual inspection of each found peak group was carried out to extract retention time (RT) intervals where a stable profile occurs at one time with peaks coelution. Such peak groups and RT-intervals detect peptide when an extracted profile of synthetic peptide (in used matrix of eight hydrolyzed non-human proteins) coincides with the profile of endogenous peptide.

ms2prot report works as an interactive document in Mozilla Firefox web browser. ms2prot reports can be viewed via HTTP online (see the table below) or downloaded as one archive, unpacked and viewed offline or shared as an ordinary document.
ms2prot report contains:

To view ms2prot reports, please, use only Mozilla Firefox web browser (or from PortableApps.com*) since only this web browser supports all the required features for displaying ms2prot reports.

ms2prot reports Detection report ZIP PASSEL
(Protocols, assays, SRM data, etc.)
PASSEL Experiments, TxGrps
(Transitions, chromatograms, d_score, etc.)
ProteomeXchange Dataset description
ms2prot-QC0 Detection-QC0.xls PASS00091 250 PXD000085 Dataset QC0 was acquired to elaborate the transition groups for the proteotypic peptides of 21 human proteins encoded by chromosome 18. SRM Data were acquired from the synthetic peptide mixtures under the conditions of slight sample overloading of the LC column.
ms2prot-bio0 Detection-bio0.xls PASS00092 750 PXD000091 Dataset bio0 was acquired to detect and quantitate proteotypic peptides of 21 human proteins encoded by chromosome 18. SRM data were acquired from 25 light endogenous peptides of Human Depleted Plasma (HPL), Human Liver (HLV) and Hep G2 cell line (HG2).
ms2prot-QC1-l Detection-QC1.xls PASS00093 410 PXD000092 Dataset QC1-l was acquired to elaborate the transition groups for the 24 proteotypic light peptides of 21 human proteins encoded by chromosome 18.
ms2prot-QC1-h Dataset QC1-h was acquired to elaborate the transition groups for the 17 proteotypic heavy peptides of 16 human proteins encoded by chromosome 18.
ms2prot-bio1 Detection-bio1.xls PASS00094 345 PXD000093 Dataset bio1 was acquired to detect and quantitate proteotypic peptides of 19 human proteins encoded by chromosome 18. SRM data acquired from 23 light endogenous peptides of Human Depleted Plasma (HPL), Human Liver (HLV) and Hep G2 cell line (HG2).

Description of SRM scouting and quality control procedures (PDF)

Measurements Structure and Statistics.xls (MS Excel 2003)

Trypsinolysis and Sample Preparation.doc (MS Word 2003)

Separation and Acquisition Protocol.doc (MS Word 2003)

See also next article.

Reports have been developed and prepared by Aleksey Filimonov for IBMC RAMS and the article in 2012.