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.