Proteomics often requires the assembly of category wide lists of things. These categories can be proteins associated with particular sequence or biological properties, post-translational modifications, or types of experiments. GPMDB can be used to generate of these lists and this page serves as an index to the lists announced for the system.

The Saccharomyces cerevisiae protein identification information in GPMDB has been summarized into a collection of spreadsheets, GPMDB Guide to the S. cerevisiae Proteome (GYP). This guide has the information organized into separate spreadsheets for each evidence code, as well as an overall listing. All of the spreadsheets are sorted by chromosome and the centrosomal naming convention commonly used for yeast ORFs. The protein accession numbers and other information was obtained from ENSEMBL's EF4.72 release of the yeast proteome. The NBS v. 2 algorithm was used to determine the evidence codes for this edition. This 2^nd edition of the Guide (GYP 2016.08.01) is available in the following formats:

The human protein identification information in GPMDB has been summarized into a collection of spreadsheets, GPMDB Guide to the Human Proteome (GHP). This guide has the information organized into separate spreadsheets for each chromosome, as well as mitochrondrial DNA. The protein accession numbers, HGNC names and chromosomal coordinates were taken from ENSEMBL v. 76 (genome assembly GRCh38). The NBS v. 2 algorithm was used to determine the evidence codes for this edition. This 22^nd edition of the Guide (GHP 2016.7.01) is available in the following formats:

The mouse protein identification information in GPMDB has been summarized into a collection of spreadsheets, the GPMDB Guide to the Mouse Proteome (GMP). This guide has the information organized into separate spreadsheets for each chromosome, as well as mitochrondrial DNA. The protein accession numbers, MGI names and chromosomal coordinates were taken from ENSEMBL v. 76 (genome assembly GRCm38). The new NBS v. 2 algorithm was used to determine the evidence codes for this edition. This 22^nd edition of the Guide (GMP 2016.7.01) is available in the following formats:

These files represent a comprehensive list of all C. elegans protein phosphorylation sites represented by good quality data in GPMDB. All of the splice variants listed by ENSEMBL have been annotated.

The files associated with the annotation for a merged list of all chromosomes is now available by FTP. A description of the format of these files (README.txt) is in the same directory. A short summary of the number of phospho-proteins, genes and sites is given here. For unique protein sequences in the proteome, the overall totals are as follows:

These files represent a comprehensive list of all D. melanogaster protein phosphorylation sites represented by good quality data in GPMDB. All of the splice variants listed by ENSEMBL have been annotated.

The files associated with the annotation for a merged list of all chromosomes is now available by FTP. A description of the format of these files (README.txt) is in the same directory. A short summary of the number of phospho-proteins, genes and sites is given here. For unique protein sequences in the proteome, the overall totals are as follows:

These files represent a comprehensive list of all S. cerevisiae protein N-terminal and lysine acetylation sites represented by good quality data in GPMDB. All of the splice variants listed by ENSEMBL have been annotated.

The files associated with the annotation and a merged list of all chromosomes are now available by FTP for lysine & N-terminal acetylation. A description of the format of these files is available in the associated "README.txt" file in in the same directory. A short summary of the number of acetylated proteins, genes and sites of each typeis given "stats/stats.txt" file.

These files represent a comprehensive list of all S. cerevisiae protein phosphorylation sites represented by good quality data in GPMDB. All of the splice variants listed by ENSEMBL have been annotated.

The files associated with the annotation for a merged list of all chromosomes is now available by FTP. A description of the format of these files (README.txt) is in the same directory. A short summary of the number of phospho-proteins, genes and sites is given here. For unique protein sequences in the proteome, the overall totals are as follows:

These files represent a comprehensive list of all Mus muscullus protein N-terminal and lysine acetylation sites represented by good quality data in GPMDB. All of the splice variants listed by ENSEMBL have been annotated.

The files associated with the annotation and a merged list of all chromosomes are now available by FTP for lysine & N-terminal acetylation. A description of the format of these files is available in the associated "README.txt" file in in the same directory. A short summary of the number of acetylated proteins, genes and sites of each typeis given "stats/stats.txt" file.

These files represent a comprehensive list of all Homo sapiens protein N-terminal and lysine acetylation sites represented by good quality data in GPMDB. All of the splice variants listed by ENSEMBL have been annotated.

The files associated with the annotation and a merged list of all chromosomes are now available by FTP for lysine & N-terminal acetylation. A description of the format of these files is available in the associated "README.txt" file in in the same directory. A short summary of the number of acetylated proteins, genes and sites of each type is given "stats/stats.txt" file.

This list is a compilation of observed serine/threonine phosphorylation sites for the Mycobacterium tuberculosis proteome (strain CDC1551), based on the data in GPMDB. This list is available in Excel spreadsheet, tab-separated text and HTML formats. It contains 41 phosphorylation sites on 35 protein sequences, with the following composition:

Each ENSEMBL splice variant protein accession number has a listing of all observed sites in a single row, that looks like the following:

We have to again thank all of the data contributors who have made these comprehensive lists possible. When using this type of information, please use normal caution. Click here for our recommendations for using lists of site assignments.

These files represent a comprehensive list of all mouse protein phosphorylation sites represented by good quality data in GPMDB. This list has been subdivided on a chromosome-by-chromosome basis, using ENSEMBL v. 71 as the source of the protein and gene sequences. All of the splice variants listed by ENSEMBL have been annotated.

The files associated with the annotation for each chromosome (and a merged list of all chromosomes) is now available by FTP. A description of the format of these files (README.txt) is in the same directory. A short summary of the number of phospho-proteins, genes and sites is given here. For unique protein sequences in the proteome, the overall totals are as follows:

As part of our contribution to the Human Proteome Project, we have compiled a comprehensive list of all human protein phosphorylation sites represented by good quality data in GPMDB. This list has been subdivided on a chromosome-by-chromosome basis, using ENSEMBL v. 70 as the source of the protein and gene sequences. All of the splice variants listed by ENSEMBL have been annotated.

The files associated with the annotation for each chromosome (and a merged list of all chromosomes) is now available by FTP. A description of the format of these files (README.txt) is in the same directory. A short summary of the number of phospho-proteins, genes and sites is given here. For unique protein sequences in the proteome, the overall totals are as follows:

We have compiled a comprehensive list of all human protein ubiquitination sites represented by good quality data in GPMDB. This list has been subdivided on a chromosome-by-chromosome basis, using ENSEMBL v. 70 as the source of the protein and gene sequences. All of the splice variants listed by ENSEMBL have been annotated.

The files associated with the annotation for each chromosome (and a merged list of all chromosomes) is now available by FTP. A description of the format of these files (README.txt) is in the same directory. A short summary of the number of ubiquitin-modified proteins, genes and sites is given here. For unique protein sequences in the proteome, the overall totals are as follows:

The GPM has been generating information about amino acid polymorphisms in model species for the last 5 years. This information has been recorded in GPMDB, which as of Jan. 1, 2013 had approximately 4.8 million observations of amino acid polymorphisms. The information about these observations has been dumped into a file, using either tab-separated value (.txt) or SQLite (.db) formats via FTP. The specific entries in these files are as follows:

The ENSEMBL protein accessions used in GPMDB can be readily assigned to specific Gene Ontology (GO) terms, using ENSEMBL's BioMart utility. These lists for all available GO terms have been constructed for three species:

The lists are divided up into the three main GO categories: biological process; cellular component; and molecular function. For each individual has an entry like:

The first column has a link to the list of proteins associated with the GO term accession number. The notation following the accession number "[n/m]" indicates that "n" proteins have been observed in GPMDB out of the "m" proteins in the proteome assigned to this category. The second category is a the controlled vocabulary description of each GO category.

The lists below were constructed from data supplied by the Normal Clinical Tissue Alliance. Proteomics data from selected studies of clinical tissue were analyzed and conservative lists of indentified proteins were constructed. The lists are organized by the best available BRENDA ontology term for the tissue, with the exception of red blood cells, which are not currently in BRENDA.

The lists given below have the proteins in plasma removed (with the exception of the plasma list).

These spreadsheets (top_1000_human_100707.xls and top_1000_mouse_100707.xls) list protein sequences that have been observed most often by GPM users who used the "human" or "mouse" ENSEMBL proteome sequences. The columns in the spreadsheet are as follows: