This week we are highlighting the three finest examples of proteomics data made public in 2012. As we have been doing for several years, we are naming the best data in three categories. N.B., these ratings do not take into account the associated publication: only the data itself was considered in these awards. Any of these data sets would be ideal for use as standards in the development of any type of bioinformatics or computational biology algorithms associated with proteomics data.

This data set consisted of 30 MS/MS data sets prepared using multidimensional chromatography and stable isotope labelling for relative quantitation. The data files were made available through PRIDE. It was published by Voegtle FN, Burkhart JM, Rao S, Gerbeth C, Hinrichs J, Martinou JC, Chacinska A, Sickmann A, Zahedi RP and Meisinger C. in Mol Cell Proteomics 2012 11:1840-52 (PubMed).

This data provided an unusually detailed look at the proteins associated with mitochrondrial metabolism in baker's yeast (see this GO protein enrichment diagram for an example of the level of enrichment obtained). The combination of good sample preparation, protein chemistry, separations and mass spectrometry allowed the investigators to accurately distinguish between background levels of protein flux and that specifically generated by the human sequence BAX:p treatment used in the experiments.

This data set consisted of 6 MS/MS data sets generated by a two step phosphoprotein/phosphopeptide affinity purification process. The data files were made available through ProteomeXchange. It was published by Hoehenwarter W, Thomas M, Nukarinen E, Egelhofer V, Roehrig H, Weckwerth W, Conrath U and Beckers GJ in Mol. Cell Proteomics November 20, 2012, mcp.M112.020560 (PubMed).

The data obtained in this study was an excellent example of combining protein and peptide separations methods to obtain samples that were highly enriched in relatively rare materials. The results obtained were very high quality, allowing the unambiguous identification of numerous biologically relevant phospho-domains in MAPK signalling related proteins.

This data set consisted of 220 MS/MS data sets, including individual multidimensional chromatography and summary results. The data files were made available through PeptideAtlas. It was published by Munoz J, Low TY, Kok YJ, Chin A, Frese CK, Ding V, Choo A, and Heck AJ in Mol Syst Biol. 2011 7:550 (PubMed).

These experiments show what can be done using quantitative mass spectrometry methods and several commonly available Orbitrap-based mass spectrometry technologies. The experiments were well executed in a consistent manner and they should be quite reproducible. If you are interested in following the concentration of any specific set of proteins in human embryonic stem cells, human-induced pluripotent stem cells or the associated precursor fibroblast cell lines, it would be a good idea to consult this data set and use it to select the appropriate technology for your experiments. While the quanitative method used in the study (lysine/N-terminus derivatization with isotope-labelled dimethyl groups) may not be as popular as some other protocols, all of the examples that we have seen have been well done, with a minimal number of side reactions and artifacts.

This data set consisted of one MS/MS data set. The data file were made available through PRIDE. It was published by Fisunov GY, Alexeev DG, Bazaleev NA, Ladygina VG, Galyamina MA, Kondratov IG, Zhukova NA, Serebryakova MV, Demina IA, and Govorun VM in PLoS One. 2011;6(7):e21964 (PubMed).

This data was interesting as it belongs to what has become a relatively rare class of results: it contains the only identification information available for many proteins from a relatively common bacterium: Acholeplasma laidlawii. A. laidlawii is a very small mycoplasma (a Mollicute genus with no cell wall), which is can pass through sterilization filters with 0.2 µm pores. It also has a small genome (~1.5 Mbp), with only 1380 genes. This single study found 819 translated proteins, a remarkable 59% of all possible translation products, including > 100 proteins current labeled as "hypothetical".

Yesterday (Thursday, November 29) we had a service interuption on many of our servers caused by a change in the Internet Protocol addresses from our internet service provider. All of the necessary changes have been made and should fully penetrate the global DNS system by the end of business today. If you still have trouble accessing a particular server or service tomorrow (December 1), please contact us and we will address the issue.

This data set consisted of 96 MS/MS data sets. The data files were made available through TRANCHE. It was published by Oppermann FS, Grundner-Culemann K, Kumar C, Gruss OJ, Jallepalli PV and Daub H in Mol Cell Proteomics 2012 11:O111.012351 (PubMed).

This data was an excellent example of how good phosphoproteomics measurements have become using CID and an Orbitrap-LTQ. The level of phosphopeptide enrichment was very high (> 80%) and multiply-phosphorylated peptides were very cleanly identified. The large neutral loss peaks that were so prominent in the first generation of phosphopeptide CID spectra have been suppressed, making the identifications straightforward without additional MS/MS/MS measurements. The sample preparation workflow used has generated phosphpeptides from a significant number of proteins with poorly understood functions, such as NDEL1:p, TPD52L2:p, EML3:p and RAI1:p, that have not been well sampled in previous large-scale phosphoproteomics experiments.

This data set consisted of 4 MS/MS data sets. The data files were made available through PRIDE. It was published by Toyofuku M, Roschitzki B, Riedel K, and Eberl L in J Proteome Res 2012 11:4906-15 (PubMed).

Pseudomonas aeruginosa is a common bacteria that thrives in many man-made environments. It is a human pathogen causing sepsis and generalized infections, particularly in individuals with weakened immune systems. This well done study provides excellent insight into the proteins produced by P.aeruginosa to form colony biofilm matrix material. The data is first rate and it is recommended for use as a reference data set for examining the challenges associated with prokaryote proteomics for both protein and peptide sequence assignment using spectra generated by CID in hybrid Orbitrap-LTQ instruments.

This data set consisted of 3 MS/MS data sets. The data files were made available through PRIDE. It was published by Goswami T, Li X, Smith AM, Luderowski EM, Vincent JJ, Rush J and Ballif BA in Proteomics 2012 12:2185-9 (PubMed).

The data from this study showed a very good group phosphopeptide identifications from murine brains, many of which were comparitively rare. The data also contained a significant subset of phosphopeptides that were multiply phosphorylated, making it interesting from the view point of the mechanics of identifying this type of peptide. The serine:threonine phosphorylation ratio for the identified peptides was ~5:1, which is a common feature of mammalian S/T-phosphorylation studies.

The Human Proteome Project has released its initial guidelines for the submission of experimental data to the project. The stated purpose of these guidelines is as follows: "At present, these guidelines lay out requirements for which types of files must be submitted where, and by implication, the minimum amount of metadata describing the generation and handling of the data, since a minimum amount of information is required to be accepted by the repositories. However, these guidelines do not specify data quality metrics that must be met, as imposed by the MCP Guidelines, for example. Such data quality metrics may become a future addition to these guidelines."

A few months ago, we launched our first attempt at hosting a set of GPMDB web services based on a REpresentational State Transfer (REST) API (see the API definition for details). This new API has been a surprising success, with over 300,000 requests made in the first two months of operation. Thanks to everyone who participated in the original Request for Comment process and the developers who have created local applications that use the available services. Please let us know if you have any suggestions for making things better, as we start the planning process for the 2.0 interface.

This data set consisted of 2 MS/MS data sets. The data files were made available through TRANCHE. It was published by Burgener A, Mogk K, Westmacott G, Plummer F, Ball B, Broliden K, and Hasselrot K in AIDS 2012 26:1857-67 (PubMed).

Unfortunately, only a limited number of the data files made available by the researchers were retrievable from TRANCHE, but the two replicates that could be downloaded were very good quality. The proteins and peptides found give an excellent guide to what can be sampled using iTRAQ quantitation of clinical samples of human saliva. Saliva is a notoriously difficult fluid to sample cleanly, but this study does an admirable job of obtaining good quality samples and analyzing them thoroughly.

This data set consisted of 18 MS/MS data sets. The data files were made available through TRANCHE. It was published by Franz-Wachtel M, Eisler SA, Krug K, Wahl S, Carpy A, Nordheim A, Pfizenmaier K, Hausser A and Macek B in Mol Cell Proteomics. 2012 11:160-70 (PubMed).

The data from this study were very good quality MS/MS spectra, representing what can be expected from any collection of well done SILAC quantitation experiments. The results support the conclusions, however our reanalysis of the data revealed a significant level of amide carbamylation. In addition to carbamylation, the paper's analysis omitted deamidation, dioxidation and N-terminal cyclization, leading to a false negative rate of >15% in the results reported in the paper. While these assignments do not affect the biological conclusions in any major way, they do have an effect on the decoy-target calculation used to estimate the peptide sequence assignment error rate. Any group interested in how false negative assignments alter the outcomes of the statistical analysis of proteomics data should examine these results carefully.

This data set consisted of 25 MS/MS data sets. The data files were made available through TRANCHE. It was published by Zhong J, Kim MS, Chaerkady R, Wu X, Huang TC, Getnet D, Mitchell CJ, Palapetta SM, Sharma J, O'Meally RN, Cole RN, Yoda A, Moritz A, Loriaux MM, Rush J, Weinstock DM, Tyner JW, and Pandey A in Mol Cell Proteomics 2012 11:M112.017764 (PubMed).

This data was obtained from a well-planned study of the protein phosphorylation dynamics of the thymic stromal lymphopoietin signalling system. The study used SILAC quantitative proteomics and affinity purification to examine the changes in protein post-translational modification involved in this particular system, which has been implicated in human disease. The SILAC method used (K6/R6) has become increasingly popular recently, challenging the dominant K8/R10 method popularized by the Mann group.

This data set consisted of 4 MS/MS data sets. The data files were made available through PRIDE. It was published by Burkhart JM, Vaudel M, Gambaryan S, Radau S, Walter U, Martens L, Geiger J, Sickmann A, and Zahedi RP in Blood 2012 120:e73-e82 (PubMed).

This data set is a good example of the depth of proteomics analysis available for simple cells. The proteome of platelets is simplified by the absence of nuclear proteins as well as proteins involved in translation and folding. Therefore, they provide an insight into the minimum set of proteins necessary to sustain cell metabolism and to perform the primary function of the platelet: the formation of blood clots. The data is high quality and the results really do provide an excellent resource for understanding the thrombocyte proteome.

The Request for Comments GPM-2011.12.14 that details a nomenclature for protein post-translational modifications has been updated to include a JSON (JavaScript Object Notation) nomenclature that parallels the original compact text version. The addition of the JSON specification was made in response to several reviewers who felt that developing parsers for the original compact text strings could be a barrier-to-use for many applications. The relative simplicity of JSON and the existence of many general-purpose JSON parsers should make the incorporation of this standard into data exchange systems somewhat easier to implement for most potential users.

This data set consisted of 8 MS/MS data sets generated from samples containing human and Pyrococcus furiosus proteins. The data files were made available through PRIDE. It was published by Vaudel M, Burkhart JM, Radau S, Zahedi RP, Martens L and Sickmann A in J. Proteome Res, 2012 11:5072-5080 (PubMed).

This data demonstrates the use of a large set of standard peptides mixed in with a sample for the purposes of quantitation. The standard peptides in this case were a whole cell digest of the proteome of Pyrococcus furiosus, an Archaea hyperthermophile. This set of peptides provided comparators present at a wide range of concentrations, with very little peptide sequence overlap with the human sample being analyzed. Even though this data was generated mainly for the purposes of a bioinformatics study, it was state-of-the-art in terms of chromatography and mass spectrometry. It was ideal for the purpose of the paper and this set of spectra should be considered as a standard for use when testing algorithms involved in proteomics data analysis and associated bioinformatics and computational biology studies.

This data set consisted of 10 MS/MS data sets generated from samples enriched in palmitoylated proteins. The data files were made available through PRIDE. It was published by Jones ML, Collins MO, Goulding D, Choudhary JS and Rayner JC in Cell Host Microbe, 2012 12:246-58 (PubMed).

This ambitious study attempts to purify palmitoylated proteins from Plasmodium falciparum schizonts obtained from Homo sapiens erythrocytes. The results show that they have generated fractions highly enriched in proteins with known palmitoylation sites from both the malaria parasite and from human red blood cell membranes. The data is unusually high quality and the methods used generated a rather complex problem in terms of peptide sequence assignments, protein identifications, computational biology and bioinformatics.

The GPM RFC 2012.09.01 that details how gene symbols will be used to reference DNA, cDNA, RNA and protein sequences has been adopted. The notation described in the RFC is meant to make discussions involving gene symbols and the macromolecule sequences associated with that gene clearer, when necessary. The notation will be used in GPM/GPMDB report pages and associated spreadsheets. This notation adds a suffix to existing gene names to specify the macromolecule, using the following convention: ":c" (cDNA); ":g" (genomic DNA); ":p" (protein) and ":r" (RNA).

This data set consisted of 2 MS/MS summaries constructed from SDS-PAGE gel bands. The data files were made available through PRIDE. It was published by Dunne JC, Li D, Kelly WJ, Leahy SC, Bond JJ, Attwood GT and Jordan TW in J Proteome Res. 2012 11(1):131-42 (PubMed).

This well done study represents the first publicly available data that details the polysaccharide-degradation proteome of one of the primary bacterial components of the ruminant digestion process, Butyrivibrio proteoclasticus. Ruminant mammals (e.g., cattle) use an elaborate series of bacterial fermentation reactions to digest plant-sourced polysaccharides into small molecules that can be used by normal mammalian digestive metabolism. The proteins identified in this study provide the best list currently available of the enzymes and transport molecules used by the microorganism to cope with the environment of the rumen.

In a potentially interesting move, the European Proteomics Association has announced on www.eupa.org that it has decided to add a new open source journal as an alternative to its current journal of choice, the Journal of Proteomics. This new publication, EuPA Open Proteomics, will be an Elsevier title under Editor-in-Chief P. Verhaert. Part of the mandate of the new journal will be to provide a forum for new types of manuscripts: "EuPA Open Proteomics will also accept direct submissions from authors wishing to report on large data sets (submitted to raw data repositories) and descriptive studies", which will be a welcome addition to the field.

The first version of a GPMDB API (Application Programming Interface) using REST (REpresentational State Transfer) services is now complete, following a very successful Request for Comments process. The full text of the service specifications is available here This version of the interface is composed of twenty-three REST services, which return information in JSON (JavaScript Object Notation) format. This format is commonly used for exchanging information with mobile devices and has become a de facto standard for internet-based APIs.

This data set consisted of 7 MS/MS analyses that were used for identification and pathway analysis. The data files were made available through TRANCHE. It was published by Pisitkun T, Gandolfo MT, Das S, Knepper MA, and Bagnasco SM in Proteomics Clin Appl. 2012 6:268-78 (PubMed).

This set of measurements nicely characterizes the proteins present in clinically isolated urinary exosomes (the membrane-bound particles shed by kidney nephrons). The proteins detected show that the exosomes contain significant amounts of molecules originating from cellular plasma membranes as well as those originating from blood plasma. The data was excellent, easy to interpret and there was no indication of significant experimental bias or artifacts in the peptides identified.

As part of our on-going relationship with the HUPO chromosome-based Human Proteome Project, we have adopted an evidence code system for reporting whether a particular protein sequence has been positively identified, indicating translation of the associated gene. This four level system has been integrated into many of the GPMDB display pages by the addition of colored symbols indicating the current status of the protein sequence associated with an accession number.

These evidence codes do not refer to the quality of an individual protein identification in a data set: they are a property of the all of information in GPMDB about a particular protein. The evidence code for any particular protein accession number can be obtained using the GPMDB REST interface and the meaning of the codes can be found a here. These codes are assigned automatically by an algorithm that considers all of the evidence in GPMDB, so the particular value of an evidence code is subject to change as the evidence for a given protein changes and as the algorithm is improved.

This data set consisted of 41 MS/MS analyses that were used both for protein identification and label-free quantitation. The data files were made available through PeptideAtlas. It was published by Malmstrom J, Karlsson C, Nordenfelt P, Ossola R, Weisser H, Quandt A, Hansson K, Aebersold R, Malmström L, and Bjorck L in J Biol Chem. 2012 287:1415-25 (PubMed).

Streptococcus pyogenes is an important human pathogen, responsible for the diseases generally classified as being caused by Group A Streptococcal (GAS) infection such as "strep throat", impetigo, necrotizing fasciitis, scarlet fever and streptococcal toxic shock syndrome. This study examined the proteome changes caused by the presence of human plasma in the cells' environment, in an attempt to understand how the organism adapts when it moves from its normal environment into human blood. The data quality is very good and the identified sequences provide good examples of the peptides available for MS-based proteomics, in the HPLC retention range of 20—40% acetonitrile.

The Human Proteome Organization's 11th Annual Congress opens tomorrow in Boston, Massachusetts. We would like to congratulate the winners of this year's HUPO Awards: Carol Robinson (Award for a Distinguished Achievement in Proteomic Sciences); Michel Desjardins (Award for Discovery in Proteomic Sciences); John Cottrell & David Creasy (Award for Science and Technology); and Mark Baker (Award for Distinguished Service).

This Request for Comment is based on a problem raised during conversations on how use gene symbols in the Human Proteome Project when referring to proteins rather than the gene. Using gene symbols for this purpose is common place in the literature, but it can be imprecise (and confusing) if the context is unclear about the type of macromolecule being referenced. A wiki page for the RFC GPM-2012.09.01 has been created. Suggestions are welcome and the period for comments ends on Sept. 14, 2012.

This data set consisted of 234 MS/MS analyses, from multidimensional chromatography experiments that used both phosphopeptide enrichment and SILAC quantitation. The data files were made available through TRANCHE. It was published by Dix MM, Simon GM, Wang C, Okerberg E, Patricelli MP, and Cravatt BF in Cell 2012 150:426-40 (PubMed).

The data from this study has the potential to provide some interesting insights into the use and reproducibility of proteomics techniques when applied to biological experiments. The work does not highlight any specific technological innovation, but it does use existing techniques well and in a routine manner. The sample preparation and handling appear to have been unusually good, with low levels of experimental artifact modifications, making the data suitable for more indepth study for the detection of rarer post-translational modifications. There are detectable levels of a few adventious proteins (bovine serum albumin, bovine casein and latex proteins), but no detectable viral proteins. There is significant sensitivity drop-off for peptides that elute prior to 20% or later than 40% acetonitrile, but this effect is consistent throughout the data.

This data set consisted of one set of selected MS/MS analyses, obtained using combined fractional diagonal chromatography (COFRADIC) to enrich methionine-containing peptides and SILAC methods for quantitation. This file were made available through PRIDE. It was published by Mestdagh P, Bostrom AK, Impens F, Fredlund E, Van Peer G, De Antonellis P, von Stedingk K, Ghesquiere B, Schulte S, Dews M, Thomas-Tikhonenko A, Schulte JH, Zollo M, Schramm A, Gevaert K, Axelson H, Speleman F and Vandesompele J in Mol Cell. 2010 Dec 10;40(5):762-73 (PubMed).

This study provides an interesting insight into how COFRADIC can be used to reduce the complexity of the peptides in protein identification experiments. The peptides found are significantly enriched in methionine, with almost 90% of the identifications containing at least one Met residue. In combination with a simple SILAC method, protein quantitation was obtained for a large number of peptides and identifications for more the 4,500 unique proteins. The use of proteomics methods inconjunction with numerous biochemical methods to study microRNA effects provided significant insight into pathway regulation in neuroblastoma cells.

This data set consisted of 1598 LC/MS analyses, including 798 MS/MS/MS runs. These files were made available through PRIDE. It was published by Bonhomme L, Valot B, Tardieu F, and Zivy M in Mol Cell Proteomics, 2012 Jul 10 (PubMed).

This interesting study contains a very large number of phosphopeptide identifications derived from the leaves of the plant Zea mays (maize). The identifications are split between conventional CID MS/MS spectra and MS/MS/MS spectra generated from the peaks corresponding to a neutral loss of -80 or -98 Da, caused by the loss of phosphate in the initial CID reaction. The study uses chemical derivatization (light and heavy dimethylation) for quantitative analysis. These careful experiments provide some interesting insights into the reaction of the plant to changes in water availability. They also are some of the best proteomics observations made to date of this commercially important species.

This data set consisted of 12 LC/MS/MS analyses from large composite MGF files constructed from the results of multidimensional chromatography experiments. These files were made available through TRANCHE. It was published by Batruch I, Smith CR, Mullen BJ, Grober E, Lo KC, Diamandis EP, and Jarvi KA in J Proteome Res. 2012 11:1503-11 (PubMed).

The data contains some of the best identitifications currently available for many proteins specific to the prostate and testis, such as PATE1, STEAP2, and TGM4. It provides a very nice set of examples of the proteins that can be reproducibly detected in seminal plasma using multidimensional chromatography methods and they can be used to develop assays for specific proteins in this clinical sample. The use of large, composite MGF files to report this type of data limits its utility for computational and quantitative biology applications, because it is impossible to determine why the detected peptides are biased against early eluting (< 20% ACN) sequences.

This data set consisted of 6 LC/MS/MS analyses composed from one dimensional SDS-PAGE bands, made available through PRIDE. It was published by Bischof S, Baerenfaller K, Wildhaber T, Troesch R, Vidi PA, Roschitzki B, Hirsch-Hoffmann M, Hennig L, Kessler F, Gruissem W, and Baginsky S in Plant Cell. 2011 23:3911-28 (PubMed).

This manuscript provides one of the largest, best sets of proteomics data from Arabidopsis thaliana cytosol ever obtained using gel electrophoresis methods. The data is almost tailor made for bioinformatics investigations and the development of peptide identification algorithms (much better than some of the truly low quality data proposed for this purpose). For such a large experiment, the data quality is consistently high and the levels of experimental artifacts are remarkably low.

This data set consisted of 8 LC/MS/MS analyses, composed from multidimensional chromatography experiments made available through TRANCHE. It was published by Gibbons JG, Salichos L, Slot JC, Rinker DC, McGary KL, King JG, Klich MA, Tabb DL, McDonald WH, and Rokas A in Curr Biol. 2012 Jul 10 (PubMed).

This data provides a remarkable insight into the changes caused by domestication in an industrial important fungus, Aspergillus oryzae. It is used to malt rice and other starch sources, a necessary step in the creation of a number of wines, spirits and sauces common in Asia. Its nearest wild relative, Aspergillus flavus, is also economically significant, however it is considered a source of spoilage in food and a common infectious agent in aspergillosis. The results presented here characterize the differences in the enzymes exported from the fungus into the environment, which the organism uses to generate small molecules for import back into its filaments. Simple inspection of the lists of proteins tell the story of how selection has been used to craft the suite of digestive enzymes secreted by the fungus, from primarily cellulose and protein digestion (A. flavus) to starch and protein (A. oryzae).

One feature of the data that was not mentioned in the article was the very high degree of non-tryptic proteolysis. Because the organisms both secrete non-specific proteases, the resulting mixture of proteins was most likely partially-digested prior to sampling and continued to have proteolytic activity during the trypsin digestion used for proteomics. This multi-step proteolysis leads to an unusual set of peptides, with 40–70% of the peptides having at least one non-tryptic cleavage and an unusual bias towards peptides with pI < 5.

This data set consisted of 100 LC/MS/MS analyses, composed of 96 one dimensional SDS-PAGE gel bands and four gel summaries, made available through PeptideAtlas as entries PAe00375, PAe003695, PAe003691, & PAe003686. It was published by Chen YS, Mathias RA, Mathivanan S, Kapp EA, Moritz RL, Zhu HJ, and Simpson RJ in Mol Cell Proteomics, 2011, 10:M110.001131 (PubMed).

The data in this study is a good example of using one-dimensional SDS-PAGE to deal with membrane proteins. The analysis of the data is straightforward and the group have done a good job of minimizing gel band contamination with the common environmental proteins human KRT1, KRT2, KRT9, and KRT10, which can be an overwhelming presence in 1D gels. The choice of Canis familiaris as the model species for the study gives an insight into the membrane proteins of a species that has not be widely used for proteomics experiments, even though its complete genome has been known for many years. The lists of proteins contain many prominent examples of proteins that are clearly present at significant levels in the organism but which remain uncharacterized (e.g., ENSCAFP00000021781, ENSCAFP00000009106, and ENSCAFP00000010256).

The main GPMDB server came back online today at 21:00 UTC. All of the tables affected were successfully restored from backup and the state of all GPMDB servers was synchronized. We made a few changes so that hopefully this situation does not recur, but we will be closely monitoring web usage for the next few days to be sure that the fixes are working. Ars longa, vita brevis.

GPMDB was taken off-line yesterday because of an unexpected very high volume of requests that caused systems problems. The affected tables are being rebuilt and we expect the server to come back on line today. If this is not possible, we will switch to backup hardware this evening. This only affects requests directly to GPMDB: all of the search services are still available and were not involved by this incident.

This data set consisted of 6 LC/MS/MS experiments, made available through PRIDE. It was published by Rashid ST, Humphries JD, Byron A, Dhar A, Askari JA, Selley JN, Knight D, Goldin RD, Thursz M, and Humphries MJ in Proteomics. 2012 May 23. doi: 10.1002/pmic.201100487 (PubMed).

This data provides a very nice insight into the extracellular matrix proteins being produced by hepatic fibroblasts. These important proteins are most often mixed together with cellular proteins in clinical tissue samples or discarded in cell culture experiments. These proteins are crucial to the formation and maintenance of tissues, but since they cannot be effectively studied using the RNA-based techniques commonly used for intracellular proteins. The data supports the conclusions in the associated manuscript, i.e., the differential presence of the relatively rare proteins WNT5A and CYR61.

The July 2012 release of the GPMDB GHP (click here) is a summary of what we know about the expression of the 63,398 gene products (including alternate-splice variants) listed by ENSEMBL, excluding all protein sequences for which the correspond RNA transcripts are marked as candidates for nonsense-mediated decay. The proteins reported in the GHP are organized by the chromosomal location of the corresponding genes. In addition to the normal complement of autosomes and sex chromosomes, the protein sequences originating on the mitochondrial chromosome and the chromosome 6 COX and QBL haplotypes are included. This seventh edition of the GHP is available as a spreadsheet or in web browser format.

GPMDB has been collecting information about amino acid polymorphisms (APs) for the last five years. The recorded information falls into two classes: APs discovered using lists of specific, known SNPs loaded from dbSNP (that we refer to as SNAPs); and APs discovered by checking all possible polymorphisms at each residue in a peptide. As of July 1, 2012 GPMDB has information on approximately 4 million observation of APs from experimental data. This information has been made available in two file formats. This information will be updated quarterly.

As of June 30, 2012, there were only twenty-eight (28) peptide sequences that had been seen more than 1,000,000 times in GPMDB. The characteristics that make a peptide eligible for the "More than a Million Club" are not completely understood, but in general they are conserved as tryptic peptides in multiple species' orthologous genes as well as alternate splices and paralogous genes, making them eligible to be seen in many different types of experiments. Here is the list of current members (click to see a list of the accession-number:#-of-observations pairs associated with each sequence):

This data set consisted of 5 LC/MS/MS experiments, made available through TRANCHE. It was published by Guyonnet B, Zabet-Moghaddam M, Sanfrancisco S, and Cornwall GA in Mol Cell Proteomics. 2012 Jun 15 (PubMed).

This data distinguishes itself by sampling a rarely examined portion of the proteome, the acrosomal matrix. This structure on sperm is responsible for attachment to the egg in the first stage of the fertilization process. The associated proteins are not commonly found in other tissues, so the samples examined here provide some of the best measurements of these molecules — such as Akap3, Akap4, Odf2, Ropn1 and all of the acrosomal dynein subunits.

The HUPO 2012 meeting in Boston Massachusetts will be held on September 9-13, 2012. The deadlines for "Late-Breaking Abstract Submission" and "Advance Registration" are both on June 30, 2012, so anyone interested in attending this event should get their information in soon. This conference will be very important in the definition and initial implementation of the chromosome- and biology/disease-based Human Proteome Projects, so anyone interested in these large-scale proteome efforts should try to attend.

This data set consisted of 2 LC/MS/MS experiments, made available through PRIDE. It was published by de Oliveira JM, van Passel MW, Schaap PJ, and de Graaff LH in PLoS One. 2011;6(6):e20865 (PubMed).

These results comprise a large fraction of the publicly available data about the Aspergillus niger proteome. While the organism is very common in the environment, it is not one of the human pathogenic Aspergillus species, such as A. fumigatus or A. flavus. A. niger is a very important industrial fungus, used mainly as a source of enzymes for food production. This study does a nice job of creating an inventory of the secreted proteins normally expressed by the organism under two common growth conditions, providing insights into the metabolic changes that are necessary for growth when the environment changes. Secreted proteins are very important for fungi as they are responsible for digesting nearby carbohydates and proteins into a form that the fungus can use as food.

We are announcing a new RFC for the development a set of web services to provide an interface for accessing information stored in GPMDB. After some research, we have chosen to use the REST architecture for these services, with JavaScript Object Notation (JSON) as the format for information returned by these services. A draft definition of a set of 14 services has been created and implemented. We would very much like to hear your comments and suggestions for additional services as well as anything you might like to suggest regarding the style, format or technology used.

The source code for the preliminary services and a demonstration client application have been made available at the GPMDB FTP site. This source code will be kept up-to-date with changes in the draft specification document.

This data set consisted of 22 LC/MS/MS experiments, made available through PRIDE. It was published by Bradel-Tretheway BG, Mattiacio JL, Krasnoselsky A, Stevenson C, Purdy D, Dewhurst S, Katze MG. in J Virol. 2011 85:8569-81 (PubMed).

The results nicely demonstrate previously unknown associations between the influenza polymerase complex and host cell proteins. The experimental strategy was well thought out and an appropriate number of replicates with and without infection were performed to confirm that the findings of the study were valid. The experiments provide some of the best observations to date of the influenza A virus RNA polymerase subunits PA, PB1 and PB2. These observations should be useful to anyone investigating the use of SRM/MRM techniques to detect these molecules in vivo. Comparison of the peptides observed for the polymerase subunits of the strain used in this study (H5N1 Vietnam/1203/04 isolate) provide an interesting case study when they are compared with those observed for other strains of the influenza virus.

This data set consisted of one composition of 2509 spectra obtained from multiple gel bands from an SDS-PAGE separation, made available through PRIDE. It was published by Ivaldi C, Martin BR, Kieffer-Jaquinod S, Chapel A, Levade T, Garin J, and Journet A in PLoS One. 2012;7(5):e37187 (PubMed).

After spending the last few weeks dealing with the complexity of large collections of mediocre data, it was a delight to find this gem. The authors have made excellent choices of the spectra to include as evidence and they have retained enough common SDS-PAGE artifact proteins so that the selected data retains the character of the original raw data. While some may be critical of this process, it does provide good insight into the quality of the experiments and the type of data used to support the conclusions in the paper. Note: CD20 and CD23 are annotated using their more modern gene names, MS4A1 and FCER2, respectively. See the HUGO Gene Nomenclature committee for CD molecules site for more information on the current status of specific "CD" genes.

As a research project, GPM and GPMDB have focussed on trying to find innovative ways to use prior biological knowledge to inform new measurements and add retrospective value to older ones. The systems that have been built therefore focus on the retention of information and knowledge, rather than the raw data used to generate that information/knowledge. Recent developments in the field suggest that relying on external, government-funded resources to retain that raw data may not be as reliable as we hoped. To address this problem, we have set up an FTP archive (ftp.proteomecentral.org) to try to maintain at least some of this data. Our first project, backing up the spectra in PRIDE, is now complete and ready for use. The files are organized by their PRIDE data set ID number and can be downloaded from the FTP site's PRIDE folder at any time.

This data set consisted of 7 result files from phospho-tyrosine enrichment experiments using SILAC methods to obtain relative quantitation. It was published by Martinez-Ferrando I, Chaerkady R, Zhong J, Molina H, Kishore H, Herbst-Robinson K, Dancy BM, Katju V, Bose R, Zhang J, Pandey A, and Cole PA in Mol Cell Proteomics. 2012 11:M111.015750. (PubMed).

This work nicely summarizes current trends in proteomics survey studies: early release of data; high resolution parent and fragment ion measurements; affinity methods to reduce sample complexity; and simple-to-interpret methods for relative quantitation. This data set was released six months prior to publication, so any issues relating to its quality or reproducibility could have been settled well before the conclusions were published. The use of an Orbitrap in "high-high" mode made the identifications easy to analyze and kept the false positive rate consistent and low (0.07-0.1%). The phospho-tyrosine peptide enrichment method used worked well and resulted in high quality phospho-domain assignments. Finally, the appropriate use of SILAC allowed the interpretation of the results to move beyond simply "yes" or "no" into a more nuanced interpretation of the effects of changing c-Src tyrosine kinase activity.

This data set consisted of 15 result files from several phospho-peptide enrichment/multidimensional chromatography experiments. It was published by Wu R, Dephoure N, Haas W, Huttlin EL, Zhai B, Sowa ME, and Gygi SP in Mol Cell Proteomics. 2011 10:M111.009654 (PubMed).

The data and experiments reported in this paper are part of a general shift in attitude towards the detection of phosphorylated domains in proteins. Most of the work in the previous decade has placed considerable emphasis on the technical aspects of identifying phosphopeptides and the qualitative reporting of their observation. This work (and that of others) is now focused on how to interpret the observation of phosphorylated protein domains in the context of a cell's biological function. The experiments performed here were well done, resulting in a nice set of protein and peptide identifications of the phosphoproteins involved in yeast metabolism.

This data set consisted of 32 LC/MS/MS experiments that were made available in mzData files via PRIDE. It was published by Thomas L, Hodgson DA, Wentzel A, Nieselt K, Ellingsen TE, Moore J, Morrissey ER, Legaie R; STREAM Consortium, Wohlleben W, Rodríguez-García A, Martín JF, Burroughs NJ, Wellington EM, and Smith MC in Mol Cell Proteomics. 2012 Feb;11(2):M111.013797 (PubMed).

These experiments give a good view into changes to the relative concentrations of many metabolic enzymes in the environmental bacterium S. coelicolor in response to changes in phosphate-containing nutrient levels. On the whole the experiments were well done, although there was significant, reproduced supression of early eluting peptides in all of the LC/MS/MS runs. This supression may have made the experiments insensitive to some particular enzymes. However, for enzymes containing observable peptides with gradient elutions > 20% acetonitrile, the relative protein regulatory responses in could be inferred with reasonable accuracy from this data set.

About a year ago (March 10, 2011), we added the capacity to associate any number of PSI-MS ontology terms with searches performed using the GPM public protein identification system. This ontology contains more than 1,200 words and phrases specifically chosen by the HUPO-PSI group. No one has used this feature of the user interface. We will be discontinuing this interface feature as of May 14, 2012, because of this lack of use. Anyone interested in maintaining this feature should send us an email (rbeavis@thegpm.org) with their concerns. We will retain an archived version of the code use to generate this list at ftp.thegpm.org/repos/thegpm/tandem/psi-ms.js.

This data set consisted of 2 LC/MS/MS experiments that were made available in mzData files via PRIDE. It was published by Tondeleir D, Lambrechts A, Mueller M, Jonckheere V, Doll T, Vandamme D, Bakkali K, Waterschoot D, Lemaistre M, Debeir O, Decaestecker C, Hinz B, Staes A, Timmerman E, Colaert N, Gevaert K, Vandekerckhove J, and Ampe C in Mol Cell Proteomics. 2012 Mar 22 (PubMed).

In this study, the authors use an unusual combination of SILAC relative quantitation and combined fractional diagonal chromatography (COFRADIC) to study what happens to mouse embryonic fibroblast cells when then lack an important cytoskeletal protein. Rather than the typical SILAC experiment in which heavy lysine and arginine residues are used, this experimental design uses heavy methionine and COFRADIC to produce fractions enriched in peptides containing oxidized methionine residues. While the use of an affinity technique has the potential to complicate quantitative experiments, these experiments seem to have worked out quite well and generated some valuable insights into the metabolic creativity shown by the fibroblasts in the face of what might seem to be an insurmountable challenge.

The good folks at ISB's PeptideAtlas have announced the availability of what they are calling the Cow PeptideAtlas, derived from a set of experiments performed by Emoke Bendixen, et al., at the Department of Animal Health and BioScience, Faculty of Agricultural Sciences, Arhus University in Denmark. This collection of identifications can be accessed using the ENSEMBL accession numbers for Bos taurus protein sequences, e.g. beta-lactoglobulin can be accessed using ENSBTAP00000019538. The data set currently available was mainly sourced from milk and colostrum. The entire data set, which also includes udder tissue, mammary epithelium and hoof dermis, can be accessed in GPMDB, using the data set keywords Bovine Peptideatlas or a protein's accession number, ENSBTAP00000019538.

This data set consisted of 3 LC/MS/MS experiments, that were made available in the form of Mascot "DAT" files via TRANCHE. It was published by König S, Nimtz M, Scheiter M, Ljunggren HG, Bryceson YT, and Jänsch L. in PLoS One. 2012 7:e29672 (PubMed).

The results presented in this study make very good use of high accuracy mass measurements of both parent and fragment ion for their biological application — determining phosphorylation changes in natural killer (NK) cells caused by changes in receptor stimulation. These cytotoxic leucocytes are known to have kinome changes associated with such stimulation, but the phosphorylation domain changes associated with specific stimulations have not been fully explored. This paper makes a start in this type of interesting, cell-specific investigation that makes use of clinically-derived cells for kinome study.

This data set consisted of 42 LC/MS/MS runs from single dimension chromatography experiments. It was published by Maier T, Schmidt A, Güell M, Kühner S, Gavin AC, Aebersold R, and Serrano L. in Mol Syst Biol 2011 7:511 (PubMed).

The data in these experiments give a good example of a straightforward analysis of the relationship between protein and mRNA concentrations in a clinically important model organism, Mycoplasma pneumoniae. The results also provide the best insights into the proteome of this prokaryote currently available, which has not be thoroughly studied even though it has a comparatively simple genome and it is one of the primary causes of atypical bacterial pneumonia. The reproducibility of this data was somewhat compromised by the consistent bias against early eluting peptides in the HPLC runs — very few peptides that would be expected to elute at < 15% acetonitrile were observed.

This data set consisted of 88 LC/MS/MS runs from multiple-dimensional chromatography experiments. It was published by Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, and Coon JJ in Nat Methods 2011 8:821-7 (PubMed).

The results here were a good representation of the proteins and phosphorylated domains that could be readily sampled in human embryonic stem cells and induced pluripotent stem cells. The techniques used were well described and the measurements were in general very good. The studies were performed using a dual-cell quadrupole linear ion trap-orbitrap hybrid mass spectrometer (dcQLT-Orbitrap), which produced high resolution, high accuracy parent and fragment ion measurements. The data was made available through the authors' lab database site, the Stem Cell-Omics Repository (SCOR).

The set of bacterial and archae proteomes made available in the main GPM interface has been updated to include 527 new proteomes from a wide variety of new species and strains, bringing the total number of available proteomes to 1,607. The new sequences have been added to all of the public search servers — you may have to refresh your browser to get the new list if you have recently used the search server web interface. This update brings the total number of prokaryote protein sequences available for identification to 5.2 million. All of the existing species and strains have had their sequences updated as well. The new sequences are available for download via FTP at ftp.thegpm.org.

A new edition of the Guide to the Human Proteome (GHP 2012.04.01) has been released. This collection is the only comprehensive listing of all of the protein sequences in the human proteome currently identified by mass spectrometry, organized by the chromosome of origin for each protein's transcript. The GHP is available in either spreadsheet or web browser (HTML) formats. The new version has some signficant improvements in the method of curation, most importantly close attention has been paid to the removal of transcripts that correspond to mRNA non-stop and nonsense-mediated decay, which significantly reduces the complexity of alternate splicing for many genes. The coverage of the GHP has been also been expanded by the 97.2 million new peptide identifications added to the underlying GPMDB data sets in the three months since the last edition (GHP 2012.01.01).

The main GPM system has been updated to use the latest version of the human proteome — ENSEMBL v. 66.37 — which was based on the human genome sequence GRCh37.p6, Feb 2009. All of the relevant resources (including annotated spectral library and proteotypic peptides) have been updated to the new sequence set. The annotation file for human sNAPs (single Nucleotide Amino acid Polymorphisms) has been updated to dbSNP 135 (1,335,299 sNAPs). Approximately 1,400 new annotations have also been added to the protein sequence-specific modification specification file based on data that has been collected by GPMDB and protein domain information.

In addition to naming an executive, the Human Proteome Project has announced the preliminary list of country affliations for the groups that will carry out the chromosome-centric HPP. The list is not yet complete, with eight chromosomes not yet assigned to particular groups. Some chromosomes, such as 12, have been assigned to multinational groups that will collaborate to generate the necessary information. The mitochondrial chromosome (MT), while listed below, is not yet an official part of the c-HPP.

The Human Proteome Project has named its Executive Committee and Senior Scientific Advisory Board. The members of these Committees will be tasked with co-ordinating the world-wide organization of the member Projects as well as making the necessary scientific decisions about how and what the member Projects will be providing to the overall project. These Committees will oversee both the chromosome-centric and the biology and disease driven Projects and the three resource Pillars: a wide array of of mass spectrometry platforms, the antibody-based Human Protein Atlas; and ProteomeXchange to integrate proteomics-based knowledge-bases.

This data set consisted of 589 LC/MS/MS runs of 1D SDS-PAGE gel bands and experimental summaries. The data was published by Steiling K, Kadar AY, Bergerat A, Flanigon J, Sridhar S, Shah V, Ahmad QR, Brody JS, Lenburg ME, Steffen M, and Spira A in PLoS One. 2009 4:e5043 (PubMed).

This excellent study contrasted the proteomes of non- and current-smokers in a very relevant tissue, bronchial airway epithelium. The results remain the definitive proteome in this clinical tissue and contains some of the best observations for a number of rarely observed proteins, such as TPPP3 (tubulin polymerization-promoting protein family member 3), SPATA18 (spermatogenesis associated 18 homolog), ODF3B (outer dense fiber of sperm tails 3B), SPA17 (sperm autoantigenic protein 17) and ENSP00000387851 (member of the ciliary rootlet coiled-coil family).

This data set consisted of 98 LC/MS/MS runs and experimental summaries. The data was published by Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, and Hynes RO in Mol Cell Proteomics 2011 mcp.M111.014647 (PubMed).

The idea behind collecting this data set was to define which proteins compose the extracellular matrix and to discover which proteins would be contributed to the extracellular matrix by the host in a xenograft experiment. The results do a good job of determining the protein complement of this material in human tissue. The xenograft experiment — growing human-source tumours in live mice — clearly shows that both the tumour cells and mouse host tissue contribute to the proteins in the tumour-associated matrix. The value of the data was somewhat reduced by the relatively large number of detectable chemical artifacts, particularly the carbamylation and carbamidomethylation of peptide N-terminii and lysine sidechains.

Because of changes at Wormbase and geneDB, these resources are no longer suitable for our uses in proteomics. The use of both of these sites and associated sequence resources will be discontinued as of May 1, 2012. They will be replaced with more useful information sources.

The RFA for a new FTP site for use by the chromosome-base Human Proteome Project has been adopted. The new site designed to satisfy the RFA's requirements (ftp.proteomecentral.org) is open and available for use. Any c-HPP group interested in using the site for data storage should simply email Ron Beavis to get their user name and password. The site is open to everyone for retrieving information — please read the terms of use and license for a better understanding of how the site is meant to be used.

The protein sequences for the Brassica rapa (turnip) ENSEMBL proteome have been added to the main search sites. This species is part of a large genus of plants that have been broadly exploited as food, but the turnip is the first genome of the genus that has been fully sequenced and interpretted.

Links to the Human Protein Reference Database (HPRD) have been removed from protein evidence display pages because of licensing problems with that site. Links to the Human Metabolome Database have also been removed from those pages, because an internal change at that site changed its behavior when searching on gene names. If anyone have any suggestions for good replacements for these resources please let us know.

This data set consisted of one large LC/MS/MS run. The data was published by Journet A, Klein G, Brugière S, Vandenbrouck Y, Chapel A, Kieffer S, Bruley C, Masselon C, and Aubry L in Proteomics. 2012 12:241-5 (PubMed).

Dictyostelium discoideum is one of the more peculiar organisms used in research. It is a free-living "slime mold", commonly found in leaf litter on any temperate forest floor. In this study the authors have characterized the proteins involved in the unusual method that the amoeboid form of this organism uses to take in nutrients from the environment: macropinocytosis. The experimental methods used were very well done and the results significantly extend what is known about both this process and the organism itself.

This data set consisted of 70 LC/MS/MS using both SDS PAGE protein and SCX peptide separation techniques. The data was published by Prasad TS, Harsha HC, Keerthikumar S, Sekhar NR, Selvan LD, Kumar P, Pinto SM, Muthusamy B, Subbannayya Y, Renuse S, Chaerkady R, Mathur PP, Ravikumar R, and Pandey A in J Proteome Res. 2012 11:247-60 (PubMed).

Candida glabrata is a haploid yeast (a.k.a., Torulopsis glabrata). It was long thought to be a human commensal organism, but it has been shown to cause pathogenic infections in immune-compromised individuals. This study of the organism's proteome, performed using FTMS with high resolution for both the parent and fragment ions, provides a nice insight into the observable proteome of this poorly studied species. It also provides an excellent set of data to compare with an existing (but relatively untested) genome sequence to discover novel genes, understand the extent of amino acid polymorphisms and compare the post-translational modification of domains with other, better studied, yeast species.

Another proposal for a Human Proteome Project has been published as a Nature Biotechnology correspondence. In this proposal, national groups will be organized to generate data and information about the proteins coded on individual chromosomes, with countries being assigned one or more chromosomes. This article describes this effort at an executive level, mainly dealing with the governance and organizational requirements of such a project. The SwissProt spin-off group, neXtprot, has been chosen as the repository for the final results of this project, with ProteomeXchange serving as the conduit for preliminary data dissemination. A web site hosted by the Institute for Systems Biology has been established for the overall HPP organization.

The first dataset that seems to be made available through ProteomeXchange has appeared in PRIDE (Pride ID 22134). This data has been annotated with the ProteomeXchange accession number PXD000001 and has an associated Digital Object Identifier (DOI) 10.6019/PXD000001. The URL associated with the DOI (http://central.proteomexchange.org/PXD000001) is currently non-functional, but hopefully that will change soon. The associated data files are currently stored on an EBI FTP site, at ftp://ftp.pride.ebi.ac.uk/2012/03/PXD000001. The normally secretive ProteomeXchange group has not acknowledged this development, but hopefully they will make some official statement about the proposed structure of the FTP site and the information to be made available through their "central.proteomexchange.org" web site following their second annual meeting in San Diego.

We will be mirroring relevant sections of the ftp.pride.ebi.ac.uk site through the GPMDB's FTP associated with the c-HPP project in the folder "proteomexchange" (ftp.proteomecentral.org/proteomexchange). ProteomeXchange accession numbers will be indexed in GPMDB and can be searched as a normal data set keyword. For example, this first entry can be accessed using http://gpmdb.thegpm.org/PXD000001 or its PRIDE ID using http://gpmdb.thegpm.org/data/keyword/PRIDE 22134.

This data set consisted of 6 LC/MS/MS runs from whole cell lysates of the organism grown under specific conditions. The data was published by Schneider K, Peyraud R, Kiefer P, Christen P, Delmotte N, Massou S, Portais JC, and Vorholt JA in J Biol Chem. 2012 287:757-66 (PubMed).

This study effectively defined the observable proteome of Methylobacterium extorquens, a Gram-negative bacterium that lives on plant leaves (click here for an amusing short presentation on this organism). Even though the title of the study suggests that the study may have limited scope, each LC/MS/MS run generated identifications for ~40% of the proteins coded in the complete genome. The analysis presented in GPMDB used the proteomes from three stains of the organism — AM1, DM4 and PA1 — to be sure that no genes were absent because of errors in the specific genome assembly of an individual strain. This analysis showed that the AM1 strain assembly was very good, with only a small number of proteins from the PA1 and DM4 proteomes found without corresponding AM1 orthologs.

This data set consisted of 181 LC/MS/MS runs from lysates of 11 different laboratory cell lines. The data was published by Geiger T, Wehner A, Schaab C, Cox J, and Mann M in Mol Cell Proteomics 2012 Jan 25 (PubMed).

If you ever wanted to know what proteins were readily observable in A549, GAMG, HEK293, HeLa, HepG2, K562, MCF7, RKO, U2OS, Jurkat, HEK293, LnCap, HeLa or K562 cells, this is the data set for you. It is probably the largest single data set generated for a publication using the current generation of Orbitrap technology. The experiments were done using HCD fragmentation and consistent chromatographic and sample preparation methods. The information is a good compliment to the earlier DSOTW Initial characterization of the human central proteome where there is overlapping information generated with conventional CID.

This data set consisted of 213 LC/MS/MS affinity purification experiments. The data was published by Hegemann B, Hutchins JR, Hudecz O, Novatchkova M, Rameseder J, Sykora MM, Liu S, Mazanek M, Lénárt P, Hériché JK, Poser I, Kraut N, Hyman AA, Yaffe MB, Mechtler K, and Peters JM in Sci Signal. 2011 4:rs12. (PubMed).

These results were good examples of the use of proteomics to target an aspect of a particular cell process, in this case the role of phosphorylation in mitosis. The experimental protocols do a good job of isolating the relavent proteins and generating easily interpretted phophopeptide spectra. The chromatography and mass spectrometry were very well done and consistent across the data set. An unusual feature of this data set was the presence of relatively strong signals from the protease domain (picornain 3C) of the human rhinovirus B-14 polyprotein. While it is known that HeLa cells are susceptible to rhinovirus (common cold) infections, this data may be the first experimental confirmation of a rhinovirus infection in cell culture based on proteomics methods.

The US National Institutes of Health have issued a Request for Information entitled "Disruptive Proteomics Technologies - Challenges and Opportunities". This RFI is part of the Common Fund initiative at the NIH. Hopefully the responses to this RFI will better inform the working group of the real issues associated with proteomics in practice. The first few paragraphs of the Purpose are given below:

The schedule for the European Proteomics Association's 2012 Basic Course program has been announced. The courses are meant to provide a theoretical basis to help students understand modern proteomics techniques; illustrate how the techniques are being applied in modern proteomics studies and provide practical instruction in laboratory techniques.

This data set consisted of 59 LC/MS/MS runs from U2-OS cell lysates. The data was published by Beck M, Schmidt A, Malmstroem J, Claassen M, Ori A, Szymborska A, Herzog F, Rinner O, Ellenberg J, and Aebersold R. in Mol Syst Biol. 2011 7:549 (PubMed).

This study provides a large set of consistently good quality, journeyman data focussed on creating a catalog of proteins present in a common cell line. The U2-OS line was derived from a female sarcoma with very few normal chromosomes and hypertriploid chromosome counts. The cell culture used appears to have relatively clean, with little if any evidence of the presence of viruses or Mycoplasma. Any group interested in quantifying unlabelled proteomics data, investigating rare post-translational modifications or developing quality control metrics should take a look at this data.

The common Repository of Adventitious Protein (cRAP) list of proteins has been updated to included three new proteins and a substitution for an obsolete sequence identifier. These changes have been made to all of the GPM search servers and the new sequence files can be obtained at ftp://ftp.thegpm.org/fasta/crap. Two of the proteins (SRPP_HEVBR and REF_HEVBR) are characteristic of contamination with latex rubber, selected based on an experimental determination of the proteins observed from macerated latex gloves (see the data here).

This data set consisted of 37 LC/MS/MS runs and summaries, from multidimensional chromatography experiments. The data was published by Barbhuiya MA, Sahasrabuddhe NA, Pinto SM, Muthusamy B, Singh TD, Nanjappa V, Keerthikumar S, Delanghe B, Harsha HC, Chaerkady R, Jalaj V, Gupta S, Shrivastav BR, Tiwari PK, and Pandey A. in Proteomics. 2011 Dec;11(23):4443-53 (PubMed).

This series of multidimensional chromatography runs using high resolution MS and HCD MS/MS did exactly what the title said: it provides a comprehensive catalogue of the proteins and consistituent peptides that are to be expected when human bile is analyzed. It contains many best-to-date observations of proteins, even ones that are not normally associated with bile, such as hornerin and dermcidin. The methods used produced surprisingly good recovery of cysteine-containing peptides, which are often depleted in proteomics measurements.

This data set consisted of 128 experiments representing LC/MS/MS runs coupled with targeted affinity purification methods. The data was published by Bantscheff M, Hopf C, Savitski MM, Dittmann A, Grandi P, Michon AM, Schlegl J, Abraham Y, Becher I, Bergamini G, Boesche M, Delling M, Dümpelfeld B, Eberhard D, Huthmacher C, Mathieson T, Poeckel D, Reader V, Strunk K, Sweetman G, Kruse U, Neubauer G, Ramsden NG and Drewes G. in Nat Biotechnol. 2011 29:255-65 (PubMed).

The results demonstrate that the best way to find and quantitate relatively rare proteins is to utilize a targeted-affinity purification approach. The protocols described in the paper work very well and the measurements were well done. The peptide identification work in the paper was rather cursory, but that does not affect the biological conclusions or the validity of the approach.

This data set consisted of 138 experiments representing LC/MS/MS runs from individual affinity purification protocols. The data was published by Glatter T, Schittenhelm RB, Rinner O, Roguska K, Wepf A, Jünger MA, Köhler K, Jevtov I, Choi H, Schmidt A, Nesvizhskii AI, Stocker H, Hafen E, Aebersold R, and Gstaiger M. in Mol Syst Biol. 2011 7:547. (PubMed).

This study was a good example of the routine use of good quality proteomics technology to elucidate an interesting aspect of biology. It examined the protein-protein interactions associated with the InR/TOR pathway in the well-established Kc167 cell line. The measurements were unambigious, resulting in a significant number of indentifications of relatively rare D. melanogaster proteins involved in this pathway. It also contained a nice survey of the detectable SNAPs present in this cell line — fruit flies have a surprisingly large number of nsSNPs compared to mammal genomes.

This data set consisted of 6 experiments from LC/MS/MS runs. The data was published by Peng L, Kapp EA, McLauchlan D, and Jordan TW. in Proteomics 2011 11:4376-84 (PubMed).

These experiments provide insight into how straightforward it has become to identify membrane proteins. Using a fairly simple sample preparation method and LC/MS/MS with an LTQ instrument, the results show that it is possible to easily identify large numbers of membrane proteins. It is still common for people to suggest that membrane proteins are "difficult" using proteomics techniques. These results show that they are really no more difficult than any other class of protein, so long as they can be kept in solution long enough to be digested.

The Request-For-Comments GPM-2011.12.14 entitled "Nomenclature for the description of protein sequence modifications" has been adopted by the GPM. The RFC describes a systematic method for recording modifications associated with protein sequences, which can also be used to formulate queries about protein modifications to any compliant database system. GPM and GPMDB will be modified over then next few months to be compliant with this new specification. We'd like to thank everyone who sent in comments, almost all of which ended up in the final version of the document.

This data set consisted of 164 experiments from multidimensional LC/MS/MS runs. The data was published by Nagaraj N, Wisniewski JR, Geiger T, Cox J, Kircher M, Kelso J, Pääbo S, and Mann M. in Mol Syst Biol. 2011 7:548 (PubMed).

This data set is an extensive investigation of how many peptides can be identified from the limited proteome of a single human cell line using a combination of straight-forward LC/MS/MS methods, multidimensional chromatography and multiple proteases, adding in high resolution MS/MS via HCD, and doing careful, consistently state-of-the-art lab work. For the large number of groups that use HeLa cells, this work should serve as a reference for what can be seen and what sort of experiment should be done to see it. For anyone interested in bioinformatics and algorithm development, the scale (> 200,000 protein identifications) and precision of the work makes it an excellent example for trying out new ideas. It is also an excellent raw data set to find novel post-translational modifications, splice variants, viral contaminants and amino acid polymorphisms.

This data set consisted of 1 SCX fraction LCMS/MS run on a Thermo Orbitrap-LTQ hybrid instrument. The data was made available on TRANCHE by the ABRF iPRG group Robert J Chalkley, Nuno Bandeira, John Cottrell, Eric Deutsch, Eugene A. Kapp, Henry H. Lam, W. Hayes McDonald and Thomas Neubert and has been described on the iPRG web site.

This rather oddball dataset provides more insight into the "chilli-cook-off" mentality associated with evaluating bioinformatics algorithms than it does into the current real-world problems in biomedical research. Tests of this sort can be useful when their goals are to provide feedback to algorithm & user interface designers and to inform users of the characteristics of algorithm performance. It is questionable as to whether any of such aims were achieved by analyzing this data set.

The data was artificially removed from context (only one of 21 SCX fractions was made available). The sample preparation methods used generated very high levels of non-enzymatic cleavage (22% of observable peptides), unusually high levels of asparagine deamination (48% of N-containing peptides) and peptide N-terminal glutamine cyclization (88% of peptides with an N-terminal Q). The mass measurements had large parent ion and fragment ion systematic errors (+5 ppm and -0.25 Da respectively) and standard deviations (4 ppm and 0.3 Da). The proteins in the sample were heavily skewed towards the cytosolic proteins and the added human sequence standard proteins (Sigma UPS). The lack of the other 20 fractions made it impossible to draw any conclusions about the relative observability of the added UPS proteins (and the ribosomal E. coli protein contaminants in the UPS preparation). It was very unclear why such a complex, poorly controlled sample/measurement combination was used to test algorithms and so little information about the true character of the sample was provided to the participating groups. This hidden complexity resulted in more of an examination of the detective abilities of the groups than a useful test of the algorithms.

The latest edition (2012.01.01) of both the GPM Homo sapiens and Mus musculus Proteome Guides have been been made available. The Guides are the results of an automated curation of the >200 million human and >50 million mouse peptide identifications in GPMDB. The Guides use ENSEMBL v. 62 protein sequences and their chromosome coordinates are aligned to the human GRCh37 genome and mouse NCBIM37 genome builds, respectively. The Guides are available either as spreadsheets or in HTML format and they may be downloaded either from the links above or the GPM Annotation Project ftp server.

This data set consisted of 4 data sets constructed from several different types of experiment. The data was published by Cappellini E, Jensen LJ, Szklarczyk D, Ginolhac A, da Fonseca RA, Stafford TW, Holen SR, Collins MJ, Orlando L, Willerslev E, Gilbert MT, and Olsen JV. in J Proteome Res. 2011 Dec 14 (PubMed).

This data was a truly amazing example of what can be obtained using samples that have simply sat around outside for 43,000 years. The preservation of the detectable peptides was unexpectedly good. The experiments were state-of-the-art at all levels and the data should be examined extensively by any group interested in detecting amino acid polymorphisms associated with evolutionary change. The analysis in the original paper was correct at the top level (the proteins detected) but was less well done at the level of amino acid polymorphisms and side chain modifications. There are several more publications' worth of information in this extraordinary data.