Quantitative Proteomics
PROMICMAPPER Platform for Quantitative Proteome Profiling
Mass spectrometry is the most powerful tool for proteomics to assess the relative abundance of proteins among biological samples. Numerous methodologies now support relative quantification measurements, providing a routine means to analyze protein expression patterns and post-translational modification states as a function of biological perturbation. Available options include label-free quantification, SILAC (stable isotope labeling by amino acids in cell culture) based quantification, and TMT (tandem mass tag) isobaric multiplex (up to 18plex) labeling quantification.
Poochon developed a standardized platform, PROMICMAPPER, for measuring changes in global protein expression in biological systems upon perturbations using isobaric mass tags and liquid chromatography tandem-mass spectrometry (LC-MS/MS). The PROMICMAPPER platform allows for the quantitative protein profiling of up to 9,000 proteins, or deep quantitative protein profiling of up to 12,000 proteins for a single project.
Additionally, the data generated by PROMICMAPPER can be analyzed using Poochon’s data and pathway analysis tool, PROMICPATH, which uses ten groups of housekeeping protein complexes to evaluate the completeness and variability of a proteome profile. The evaluation ensures the integrity, reliability, and reproducibility of a large set of protein profile data generated by PROMICMAPPER.
PROMICMAPPER is the most cost-efficient approach for identification of differential expression of proteins for elucidating the molecular mechanisms of perturbations and discovery of biomarkers.
Quantitative Comparison of the Proteome (Up to 9,000 Proteins) Of 6-18 Samples in One Set of Analysis Using Isobaric Mass Tags
Price: $1,000 per sample
Turnaround Time: 15 to 20 business days
Service Description
• Identification and quantification of the proteome expressed by a cell, tissue, or organism for up to 18 samples in one simultaneous analysis using Isobaric Mass Tags
• Up to 9,000 proteins identified at 1% FDR
• Profile evaluated for integrity and variability using PROMICPATH
• Workflow: Protein lysate preparation, enzymatic digestion, TMT labeling, UHPLC fractionation, LC-MS/MS analysis, TMT quantitation, data analysis, and results report
Deliverables
• Proteome Profiling Report
• List of identified proteins with TMT labeling based relative abundance
• List of all identified proteins with matched peptides sequences
• List of proteins that are differentially expressed among samples (e.g., > 2 folds)
• Data normalization, statistical analysis, volcano plots, heat maps
• Data figures
• Raw data files, upon request
Suitable Sample Type
• Fresh frozen cell pellet (≥ 2 million cells per sample recommended for optimal results)
• Fresh frozen tissue (≥ 100 mg recommended for optimal results)
• Total cell or tissue lysate (≥ 200 μg of total protein recommended for optimal results)
• Identification and quantification of the proteome expressed by a cell, tissue, or organism for up to 18 samples in one simultaneous analysis using Isobaric Mass Tags
• Up to 9,000 proteins identified at 1% FDR
• Profile evaluated for integrity and variability using PROMICPATH
• Workflow: Protein lysate preparation, enzymatic digestion, TMT labeling, UHPLC fractionation, LC-MS/MS analysis, TMT quantitation, data analysis, and results report
• Proteome Profiling Report
• List of identified proteins with TMT labeling based relative abundance
• List of all identified proteins with matched peptides sequences
• List of proteins that are differentially expressed among samples (e.g., > 2 folds)
• Data normalization, statistical analysis, volcano plots, heat maps
• Data figures
• Raw data files, upon request
• Fresh frozen cell pellet (≥ 2 million cells per sample recommended for optimal results)
• Fresh frozen tissue (≥ 100 mg recommended for optimal results)
• Total cell or tissue lysate (≥ 200 μg of total protein recommended for optimal results)
Proteome Profiling (Up to 9,000 Proteins per Sample) From Tissue or Cell Line Samples Using Label-Free Quantitation Method
Price: $3,000 per sample
Turnaround Time: 15 to 20 business days
Service Description
• Identification and quantification of the entire set of proteins (the proteome) expressed by a cell, tissue or organism
• Up to 9,000 proteins identified at 1% FDR from one sample
• The profile is evaluated for integrity and variability using PROMICPATH
• Workflow: Protein lysate preparation, enzymatic digestion, UHPLC fractionation (12 fractions), or SDS-PAGE gel fractionation, twelve LC-MS/MS 110 minute runs, data analysis, and results report
Deliverables
• Proteome Profiling Report
• List of identified proteins with label-free PSM# based relative abundance
• List of all identified proteins with matched peptides sequences
• List of proteins that are differentially expressed among samples (e.g., > 2 folds)
• Data normalization, statistical analysis, volcano plots, heat maps
• Data figures
• Raw data files, upon request
Suitable Sample Type
• Fresh frozen cell pellet (≥ 5 million cells per sample recommended for optimal results)
• Fresh frozen tissue (≥ 100 mg recommended for optimal results)
• Total cell or tissue lysate (≥ 200 μg of total protein recommended for optimal results)
• Identification and quantification of the entire set of proteins (the proteome) expressed by a cell, tissue or organism
• Up to 9,000 proteins identified at 1% FDR from one sample
• The profile is evaluated for integrity and variability using PROMICPATH
• Workflow: Protein lysate preparation, enzymatic digestion, UHPLC fractionation (12 fractions), or SDS-PAGE gel fractionation, twelve LC-MS/MS 110 minute runs, data analysis, and results report
• Proteome Profiling Report
• List of identified proteins with label-free PSM# based relative abundance
• List of all identified proteins with matched peptides sequences
• List of proteins that are differentially expressed among samples (e.g., > 2 folds)
• Data normalization, statistical analysis, volcano plots, heat maps
• Data figures
• Raw data files, upon request
• Fresh frozen cell pellet (≥ 5 million cells per sample recommended for optimal results)
• Fresh frozen tissue (≥ 100 mg recommended for optimal results)
• Total cell or tissue lysate (≥ 200 μg of total protein recommended for optimal results)
Proteome Profiling (Up to 12,000 Proteins per Sample) From Tissue or Cell Line Samples Using the Label-Free Quantitation Method
Price: $4,200 per sample
Turnaround Time: 15 to 20 business days
Service Description
• Identification and quantification of the entire set of proteins (the proteome) expressed by a cell, tissue or organism
• Up to 12,000 proteins identified at 1% FDR from one sample
• Proteome profile is evaluated for integrity and variability using PROMICPATH
• Workflow: Protein lysate preparation, enzymatic digestion, UHPLC fractionation (24 fractions), twenty-four LC-MS/MS 110 minute runs, data analysis, and results report
Deliverables
• Proteome Profiling Report
• List of identified proteins with label-free PSM# based relative abundance
• List of all identified proteins with matched peptides sequences
• List of proteins that are differentially expressed among samples (e.g., > 2 folds)
• Data normalization, statistical analysis, volcano plots, heat maps
• Data figures
• Raw data files, upon request
Suitable Sample Type
• Fresh frozen cell pellet (≥ 10 million cells per sample recommended for optimal results)
• Fresh frozen tissue (≥ 100 mg recommended for optimal results)
• Total cell or tissue lysate (≥ 500 μg of total protein recommended for optimal results)
• Identification and quantification of the entire set of proteins (the proteome) expressed by a cell, tissue or organism
• Up to 12,000 proteins identified at 1% FDR from one sample
• Proteome profile is evaluated for integrity and variability using PROMICPATH
• Workflow: Protein lysate preparation, enzymatic digestion, UHPLC fractionation (24 fractions), twenty-four LC-MS/MS 110 minute runs, data analysis, and results report
• Proteome Profiling Report
• List of identified proteins with label-free PSM# based relative abundance
• List of all identified proteins with matched peptides sequences
• List of proteins that are differentially expressed among samples (e.g., > 2 folds)
• Data normalization, statistical analysis, volcano plots, heat maps
• Data figures
• Raw data files, upon request
• Fresh frozen cell pellet (≥ 10 million cells per sample recommended for optimal results)
• Fresh frozen tissue (≥ 100 mg recommended for optimal results)
• Total cell or tissue lysate (≥ 500 μg of total protein recommended for optimal results)
+ P201: Tandem Mass Tag Labeling Quantitative Proteome Profiling
Quantitative Comparison of the Proteome (Up to 9,000 Proteins) Of 6-18 Samples in One Set of Analysis Using Isobaric Mass Tags
Price: $1,000 per sample
Turnaround Time: 15 to 20 business days
Service Description
• Identification and quantification of the proteome expressed by a cell, tissue, or organism for up to 18 samples in one simultaneous analysis using Isobaric Mass Tags
• Up to 9,000 proteins identified at 1% FDR
• Profile evaluated for integrity and variability using PROMICPATH
• Workflow: Protein lysate preparation, enzymatic digestion, TMT labeling, UHPLC fractionation, LC-MS/MS analysis, TMT quantitation, data analysis, and results report
Deliverables
• Proteome Profiling Report
• List of identified proteins with TMT labeling based relative abundance
• List of all identified proteins with matched peptides sequences
• List of proteins that are differentially expressed among samples (e.g., > 2 folds)
• Data normalization, statistical analysis, volcano plots, heat maps
• Data figures
• Raw data files, upon request
Suitable Sample Type
• Fresh frozen cell pellet (≥ 2 million cells per sample recommended for optimal results)
• Fresh frozen tissue (≥ 100 mg recommended for optimal results)
• Total cell or tissue lysate (≥ 200 μg of total protein recommended for optimal results)
• Identification and quantification of the proteome expressed by a cell, tissue, or organism for up to 18 samples in one simultaneous analysis using Isobaric Mass Tags
• Up to 9,000 proteins identified at 1% FDR
• Profile evaluated for integrity and variability using PROMICPATH
• Workflow: Protein lysate preparation, enzymatic digestion, TMT labeling, UHPLC fractionation, LC-MS/MS analysis, TMT quantitation, data analysis, and results report
• Proteome Profiling Report
• List of identified proteins with TMT labeling based relative abundance
• List of all identified proteins with matched peptides sequences
• List of proteins that are differentially expressed among samples (e.g., > 2 folds)
• Data normalization, statistical analysis, volcano plots, heat maps
• Data figures
• Raw data files, upon request
• Fresh frozen cell pellet (≥ 2 million cells per sample recommended for optimal results)
• Fresh frozen tissue (≥ 100 mg recommended for optimal results)
• Total cell or tissue lysate (≥ 200 μg of total protein recommended for optimal results)
+ P202: Label-Free Quantitative Proteome Profiling
Proteome Profiling (Up to 9,000 Proteins per Sample) From Tissue or Cell Line Samples Using Label-Free Quantitation Method
Price: $3,000 per sample
Turnaround Time: 15 to 20 business days
Service Description
• Identification and quantification of the entire set of proteins (the proteome) expressed by a cell, tissue or organism
• Up to 9,000 proteins identified at 1% FDR from one sample
• The profile is evaluated for integrity and variability using PROMICPATH
• Workflow: Protein lysate preparation, enzymatic digestion, UHPLC fractionation (12 fractions), or SDS-PAGE gel fractionation, twelve LC-MS/MS 110 minute runs, data analysis, and results report
Deliverables
• Proteome Profiling Report
• List of identified proteins with label-free PSM# based relative abundance
• List of all identified proteins with matched peptides sequences
• List of proteins that are differentially expressed among samples (e.g., > 2 folds)
• Data normalization, statistical analysis, volcano plots, heat maps
• Data figures
• Raw data files, upon request
Suitable Sample Type
• Fresh frozen cell pellet (≥ 5 million cells per sample recommended for optimal results)
• Fresh frozen tissue (≥ 100 mg recommended for optimal results)
• Total cell or tissue lysate (≥ 200 μg of total protein recommended for optimal results)
• Identification and quantification of the entire set of proteins (the proteome) expressed by a cell, tissue or organism
• Up to 9,000 proteins identified at 1% FDR from one sample
• The profile is evaluated for integrity and variability using PROMICPATH
• Workflow: Protein lysate preparation, enzymatic digestion, UHPLC fractionation (12 fractions), or SDS-PAGE gel fractionation, twelve LC-MS/MS 110 minute runs, data analysis, and results report
• Proteome Profiling Report
• List of identified proteins with label-free PSM# based relative abundance
• List of all identified proteins with matched peptides sequences
• List of proteins that are differentially expressed among samples (e.g., > 2 folds)
• Data normalization, statistical analysis, volcano plots, heat maps
• Data figures
• Raw data files, upon request
• Fresh frozen cell pellet (≥ 5 million cells per sample recommended for optimal results)
• Fresh frozen tissue (≥ 100 mg recommended for optimal results)
• Total cell or tissue lysate (≥ 200 μg of total protein recommended for optimal results)
+ P203: Comprehensive Label-Free Quantitative Proteome Profiling
Proteome Profiling (Up to 12,000 Proteins per Sample) From Tissue or Cell Line Samples Using the Label-Free Quantitation Method
Price: $4,200 per sample
Turnaround Time: 15 to 20 business days
Service Description
• Identification and quantification of the entire set of proteins (the proteome) expressed by a cell, tissue or organism
• Up to 12,000 proteins identified at 1% FDR from one sample
• Proteome profile is evaluated for integrity and variability using PROMICPATH
• Workflow: Protein lysate preparation, enzymatic digestion, UHPLC fractionation (24 fractions), twenty-four LC-MS/MS 110 minute runs, data analysis, and results report
Deliverables
• Proteome Profiling Report
• List of identified proteins with label-free PSM# based relative abundance
• List of all identified proteins with matched peptides sequences
• List of proteins that are differentially expressed among samples (e.g., > 2 folds)
• Data normalization, statistical analysis, volcano plots, heat maps
• Data figures
• Raw data files, upon request
Suitable Sample Type
• Fresh frozen cell pellet (≥ 10 million cells per sample recommended for optimal results)
• Fresh frozen tissue (≥ 100 mg recommended for optimal results)
• Total cell or tissue lysate (≥ 500 μg of total protein recommended for optimal results)
• Identification and quantification of the entire set of proteins (the proteome) expressed by a cell, tissue or organism
• Up to 12,000 proteins identified at 1% FDR from one sample
• Proteome profile is evaluated for integrity and variability using PROMICPATH
• Workflow: Protein lysate preparation, enzymatic digestion, UHPLC fractionation (24 fractions), twenty-four LC-MS/MS 110 minute runs, data analysis, and results report
• Proteome Profiling Report
• List of identified proteins with label-free PSM# based relative abundance
• List of all identified proteins with matched peptides sequences
• List of proteins that are differentially expressed among samples (e.g., > 2 folds)
• Data normalization, statistical analysis, volcano plots, heat maps
• Data figures
• Raw data files, upon request
• Fresh frozen cell pellet (≥ 10 million cells per sample recommended for optimal results)
• Fresh frozen tissue (≥ 100 mg recommended for optimal results)
• Total cell or tissue lysate (≥ 500 μg of total protein recommended for optimal results)
submission Guidelines
