1. What is the human brain proteome map portal?
  The human brain proteome map portal is an online resource available publicly for visualization of the high-resolution mass spectrometry-based proteomics data from 32 adult human brain sub-regions. It also includes data from a temporal study quantifying proteins expressed in 4 different sub-regions of human brain. This initiative aims to provide an in-depth understanding of the proteins expressed across different sub-regions of the human brain.
2. Are these data from individuals with any known diseases?
  The brain regions used in the study were obtained from individuals with no known history of neurological disorders.
3. What is the timeline adopted for the temporal study conducted for the Developmental Brain Proteome dataset? How is the expression of proteins quantified?
  The sample set includes pre-natal, infant, child, adult and geriatric human brain from four different sub regions namely, Dorsolateral pre-frontal cortex, Cerebellum, Hippocampus and Thalamus. The time points used are 22 weeks, 26 weeks, 1 year, 2 years, 4 years, 22 years, 35 years, 42 years and 82 years. We quantified the relative abundance of the proteins expressed in each sub-region using a Tandem Mass Tag (TMT) labeling based-quantitative proteomics approach.
4. What is the quality of data?
  All data were acquired on high-resolution Orbitrap Fusion Tribrid mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) using HCD method for fragmentation. The data were searched against decoy database with a 1 % FDR cut off at peptide and PSM level.
5. How are the expression values calculated for the Human Brain Proteome data set?
  The expression values were calculated by intensity based absolute quantification method (iBAQ)
6. Which version of reference database has been used for searching the proteomics data?
Mass spectrometry derived data were searched against Human RefSeq 75 database (consisting of 36,691 entries along with common contaminants) through Proteome Discoverer 2.1 (Thermo Scientific, Bremen, Germany) using SEQUEST HT and Mascot search algorithms.
7. Can I query for more than one gene at a time? Can I query for one gene in more than a sub-region at a time?
  Single as well as multiple gene symbols can be queried for visualizing the expression patterns across different sub-regions. The user can also specify (check or uncheck) brain sub-regions for visualizing the expression levels of the gene/genes of their interest.
8. How is the expression level of a gene displayed?
  The relative expression profile of a queried gene is displayed as a heatmap at the protein level. This can be further explored to check the number of peptides identified and the relative expression in all the sub-regions.
9. How do I download mass spectrometry-based results from the portal?
  The Human Brain Proteome results can be downloaded from the portal by Academic and Non-academic users. The user is required to fill in the details under the Download tab in the portal.
10. How do I download mass spectrometry-based data (.raw files, search results) of Human Brain Proteome Project?
  All the mass spectrometry proteomic data have been submitted to the ProteomeXchange Consortium via the PRIDE partner repository. The data can be downloaded using the dataset identifier PXDxxxxxx.
11. How is the expression level of a protein displayed for developmental brain regions?
  The protein abundance values for each age groups within a given region were preprocessed with normalization followed by batch correction (for detail method please refer to the manuscript). The average values were calculated for each age groups from the replicates. The average values were scaled to log10 for plotting.
12. How can I cite the Human Brain Proteome Map portal?
13. How can I contact if there are some questions about the Human Brain Proteome portal?
  Any queries can be submitted to the Contact Us tab along with the contact details of the user.

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