GPMDB Data set of the week

The GPMDB contains thousands of data sets contributed by researchers around the world. Every week, we select a data set because of its technical excellence, biological interest or simply because we think it is of general interest to the proteomics community.

Data set of the week archives

Data set of the week: (2010/08/29)
Human Ccr4-Not complexes contain variable deadenylase subunits.

This data set contains nine (9) LC/MS/MS analyses. The original manuscript describing this work was published by Lau NC, Kolkman A, van Schaik FM, Mulder KW, Pijnappel WW, Heck AJ, and Timmers HT. in Biochem J. 2009 422:443-53 (PubMed).

The study contained eight (8) pulldown experiments and one (1) control. Each pull-down is annotated with the bait protein. The experiment uses the combination of Lys-C and bovine trypsin characteristic of the Heck group, which generates a rather complete set of tryptic peptides, although there were a signficant number of non-tryptic peptides generated. The sample preparation method used urea, so there was also a significant number of carbamylated peptides detected. Neither of these artifacts affect the conclusions of the study.

The study contains also contains a surprising number of protein identifications that are the best so far obtained in GPMDB, e.g., TNKS1BP1, RAVER1, FHL2, RQCD1, RNF219, UBAP2L, BAG3 as well as the bait CNOT proteins. Pull-down experiments, with their ability to purify an unusual fraction of proteins, seem to be very effective at obtaining the best observations of rare proteins, compared to large MudPit-style survey experiments.

Data set of the week: (2010/08/22)
Low abundance proteome of human red blood cells captured by combinatorial peptide libraries. Behavior of mono- to hexapeptides.

This data set contains 19 LC/MS/MS analyses. The original manuscript describing this work was published by Sim C, Bachi A, Cattaneo A, Guerrier L, Fortis F, Boschetti E, Podtelejnikov A, and Righetti PG. in Anal Chem 2008 80:3547-56 (PubMed).

This study is an excellent example of a very important class of study: attempting to use novel separation strategies to increase the dynamic range of tissue proteomics. The particular strategy used in this case appears to work quite well at obtaining distributions of proteins with limited specificity, while at the same time producing fractions depleted in high abundance proteins. Technically, the data is also very quality and it contains an unusual number of high confidence identifications of relatively small peptides (< 1000 Da).

Data set of the week: (2010/08/15)
Quantitative analysis of kinase-proximal signaling in lipopolysaccharide-induced innate immune response.

This data set contains 73 LC/MS/MS data sets of obtained from mouse RAW 264.7 cells (macrophage cell line) that have been treated with lipopolysaccharide to simulate infection with Gram-negative bacteria. This data was published by Sharma K, Kumar C, Kéri G, Breitkopf SB, Oppermann FS, and Daub H in J Proteome Res. 2010, 9:2539-49 (PubMed).

The goal of the paper was to follow TOLL-like receptor phospho-signaling during this sort of simulated infection using SILAC: a combination of unlabelled and labelled samples with two different isotopic tag pairs (K(4),R(6) and K(8)R(10)) were used to detect differential protein and phosphopeptide concentrations.

In addition to the biological conclusions, this data contains some excellent examples of a common analytical artifact associated with the use of titanium dioxide phosphopeptide enrichment. Metal oxide columns work by binding peptides with low pIs (i.e., acidic peptides). While phosphopeptides certainly fill the bill as being acidic relative to most peptides, normal peptide sequences with multiple acidic sidechains are also strongly enriched by these columns. This effect can be clearly seen by using the pI vs. RT and the amino acid analysis displays. In example used here, most of the peptides detected have a pI < 5. Aspartic acid (D) and glutamic acid (E) residues in the detected peptides are enriched to 250% and 215% of their expected composition, based on the composition of the associated proteins.

Data set of the week: (2010/08/08)
Comparative proteome profiling of Mycobacterium tuberculosis: the response of drug-resistant and drug-sensitive stains.

This data set contains 6 (six) MudPit data sets of two different strains of M. tuberculosis, A12998 (daughter strain, drug-resistant) and A7494 (parent strain, drug-sensitive). This data was published via upload to Peptidome as Study PSE133 by Moo-Jin Suh, Rembert Pieper, and Shih-Ting Huang from the J. Craig Venter Institute.

From Peptidome: The study describes the analysis of proteins from Drug-resistant and -sensitive strains of Mycboacterium tuberculosis. LC-MS-based proteomics approach was combined with APEX to quantitatively measure relative proteins abundance and to compare the cellular protein composition of Mycobacterium tuberculosis strains A12998 (daughter strain, drug-resistant) and A7494 (parent strain, drug-sensitive).

The results are probably the most thorough analysis of proteins from this important pathogen and they make up a large fraction of the Annotated Spectrum Libraries available from M. tuberculosis strains.

An unexpected piece of information made available through this data set is a good initial measurement of the phosphoproteome of this prokaryote. M. tuberculosis is known to have a serine/threonine kinase and this data set has a number of very good phophopeptides generated by this kinase. The kinase appears to prefer threonine phosphorylation, with a S:T ratio of about 1:3. This ratio is the reverse of typical eukaryote kinases, which seem to prefer serine by about 3:1. The phosphoproteome generated from this study is available in either Excel, html or tab-separated text formats, as projected on to the proteome of strain CDC1551. Note: the original analysis in Peptidome did not include phosphorylation, so these results are only present in the GPMDB re-analysis. It would be very useful to have an IMAC-type study done on these and other M. tuberculosis strains.

Data set of the week: (2010/08/01)
In-depth proteomic analyses of direct expressed prostatic secretions.

This data set contains 9 (nine) MudPit data sets, each measured from a different prostatic fluid sample from individuals with prostate cancer. The original raw data was obtained from TRANCHE. It was published by Drake RR, Elschenbroich S, Lopez-Perez O, Kim Y, Ignatchenko V, Ignatchenko A, Nyalwidhe JO, Basu G, Wilkins CE, Gjurich B, Lance RS, Semmes OJ, Medin JA, and Kislinger T. in J Proteome Res. 2010, 9:2109-16 (PubMed).

The results show the amount of variability that can be expected when analyzing biological replicates of clinically sampled material. The identifications were very high quality and are the best quality measurements of many rather rare proteins, such as KLK3 (prostate-specific antigen) and ACPP (Prostatic acid phosphatase). The data shows moderate levels of carbamylation from the urea solublization method used. There were also significant concentrations of peptides generated by non-tryptic cleavage, probably from the presence of proteases in the sample itself as the cleavage sites were not chymotryptic. An examination of the AAA page (e.g., sample #2) showed that the "Pre" and "C-terminal" columns were broadly populated for most residues, not just the K and R residues normally expected in a trypsin cleavage experiment.

Interestingly for a sample obtained from prostate secretions, no proteins originating from genes on the Y chromosome were detected. This fact points out a general feature of proteomics: there does not seem to be any "common sense" association between tissue-specific protein concentrations and chromosomes.

Data set of the week: (2010/07/25)
Proteomic analysis of the secretome of human umbilical vein endothelial cells using a combination of free-flow electrophoresis and nanoflow LC-MS/MS.

This data set contains a single LC/MS/MS data set, using a combination of free-flow electrophoresis and nanoflow HPLC separations. The original raw data was made available as a Scaffold file from a web site maintained by the authors (www.vascular-proteomics.com). It was published by Tunica DG, Yin X, Sidibe A, Stegemann C, Nissum M, Zeng L, Brunet M, and Mayr M in Proteomics. 2009, 9:4991-6 (PubMed).

This study attempts to discover a difficult thing: the secretome of human umbilical vein endothelial cells in the face of the background proteins in a complex growth medium. The results provide a good basis for the examination of this important cell type, with a very good set of identifications that provides a broad survey of the proteins that can be readily obtained from these cells.

Data set of the week: (2010/07/18)
Proteomics Analysis of the Causative Agent of Typhoid Fever.

This data set contains 313 LC/MS/MS runs using Thermo LTQ mass spectrometers. The original raw files originally from the Resource Center for Biodefense Proteomics Research, which has been superceded by the Pathogen Portal (raw data). It was published by Ansong C, Yoon H, Norbeck AD, Gustin JK, McDermott JE, Mottaz HM, Rue J, Adkins JN, Heffron F, and Smith RD in J Proteome Res. 2008, 7:546-57 (PubMed).

This very thorough data set is the primary large collection of information that has allowed for the creation of the rather comprehensive annotated spectrum libraries that are now available for S. enterica related species, including S. typhi and S. typhimurium. The Pacific Northwestern National Laboratory group was an early proponent of making publicly-funded proteomics raw data widely available and their efforts legitimized the idea for many other groups.

Data set of the week: (2010/07/11)
Discovery of Anthrax Biomarkers Using Label-Free Quantitative Phosphoproteomics via Mass Spectrometry.

This data set contains 66 individual phosphopeptide enriched LC/MS/MS runs made using a Thermo Orbitrap hybrid mass spectrometer. The original raw files were transferred from TRANCHE. The data was credited to Nathan P. Manes, Li Dong, Weidong Zhou, Xiuxia Du, Nikitha Reghu, Arjan C. Kool, Dahan Choi, Charles L. Bailey, Emanuel F. Petricoin III, Lance A. Liotta, and Serguei G. Popov. It was made available prior to publications, although some part of the data was presented at the 2010 ASMS conference.

The analyzed results are simply the best, most consistent set of phosphopeptide results that we have ever seen. The combination of sample preparation, HPLC and mass spectrometry used by the authors has generated what can only be considered a milestone in the application of phospho-proteomics technique to real tissue samples.

Data set of the week: (2010/07/04)
Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions.

This data set contains 61 individual experiments using both SILAC and label-free quantitation. The experimental protocols used either trypsin or endo-LysC to digest the proteins, depending on the type of protocol being used. The original raw files were transferred from TRANCHE via ProteomExchange. The data was published by Hubner NC, Bird AW, Cox J, Splettstoesser B, Bandilla P, Poser I, Hyman A, Mann M in J Cell Biol. 2010 189:739-54 (PubMed).

The data was generated to demonstrate the utility of a new technique for protein quantitation developed by the authors: "quantitative BAC-green fluorescent protein interactomics" (QUBIC). The technique is meant to be applied to the quantitative study of protein-protein interactions, several of which are demonstrated here. The technical quality of the MS/MS data is excellent, with many ids for individual proteins in the top 10% of all GPMDB observations.

Data set of the week: (2010/06/27)
mTAL Phosphoproteome Data.

This data set contains metal oxide enriched LC/MS/MS observations of phosphopeptides from R. rattus medullary Thick Ascending Limb (mTAL) cells. The raw files were transferred from TRANCHE via ProteomExchange. The original analysis was reported by Ruwan Gunaratne, Guozhong Ma, Trairak Pisitkun, and Mark A. Knepper as part of the mTAL-PD project. It appears to be closely related to the Collecting Duct Phosphoproteome Database.

The phosphorylated domains obtained are interesting because there is surprisingly little publicly available data from rat cell lines or tissue samples. The phosphopeptide enrichment here was somewhat less effective than in some other studies, however overall it is quite typical of IMAC phosphopeptide enrichment studies. This study has significantly added to the known phosphorylated domains for available R. rattus through GPMDB's pSYT interface.

Data set of the week: (2010/06/20)
Proteomic analysis of mouse brain microsomes: identification and bioinformatic characterization of endoplasmic reticulum proteins in the mammalian central nervous system.

This data set contains 1 2DLC MS/MS and 3 1DLC MS/MS runs obtained from mouse brain microsomal preparations. The original data was transferred from TRANCHE via ProteomExchange. The original data analysis was reported by Stevens SM Jr, Duncan RS, Koulen P, Prokai L. in J Proteome Res. 2008 7:1046-54. (PubMed).

This data set is interesting in a number of ways. It shows the difference in the depth of analysis available using of multi-dimensional chromatographic analysis versus simple, single separation HPLC. The three repetitions of the 1D LCMS approach give a good indication of the statistical variability that is to be expected caused by the under-sampling inherent in this type of measurement. A Gene Ontology analysis of the data (e.g., GPM33080005862) shows the complexity of real microsomal samples, compared to simply believing that they contain only membrane and membrane-associated proteins. A similar study can be compared, showing some significant differences in microsome proteome composition, which are most likely due to variations in the sample preparation methods.

Data set of the week: (2010/06/13)
The minor salivary gland proteome in Sjögren's syndrome.

This data set contains 2 LC-MS-MS runs obtained from human salivary gland tissue. The original data was transferred from PRIDE entries 7962-3 via ProteomExchange. The data was reported by Hjelmervik TO, Jonsson R, Bolstad AI. in Oral Dis. 2009 15:342-53. (PubMed).

The two sets of identifications are meant to show the differences in the protein compliment of salivary glands caused by the autoimmune disease, Sjögren's syndrome. Technically, the data is a good example of the use of a high resolution MS/MS device (ESI-QTOF, Ultima Global) applied to tissue samples. The high accuracy fragment ion masses significantly improve the quality of the identifications.

Data set of the week: (2010/06/06)
Identification of Ricin and Concanavalin A-binding Trypanosoma brucei Glycoproteins.

This data set contains 1 data set obtained from T. brucei. The original data was transferred from PRIDE 9223 via ProteomExchange. A portion of the data was report by Izquierdo L, Schulz BL, Rodrigues JA, Güther ML, Procter JB, Barton GJ, Aebi M, Ferguson MA in EMBO J. 2009 28:2650-61 (PubMed).

The data was obtained by using the the lectins concanavalin A and ricin to pull down glycoproteins from T. brucei (blood stream form) and then glycosidases were used to remove the N-linked glycosylation, leaving a deamidated asparagine residue behind. Any deamidated N residue that was associated with the N-{P}-[ST] glycosylation motif should be considered a potential N-linked glycosylation site. You can see just these peptides by clicking here.

Data set of the week: (2010/05/30)
Use of fluorescence-activated vesicle sorting for isolation of naked2-associated, basolaterally-targeted exocytic vesicles for proteomic analysis.

This data set contains 6 experiments obtained from C. familiaris and it is probably the best single data set we have in GPMDB from the domestic dog proteome. This work was transferred from TRANCHE via ProteomExchange and it was published by Cao Z, Li C, Higginbotham JN, Franklin JL, Tabb DL, Graves-Deal R, Hill S, Cheek K, Jerome WG, Lapierre LA, Goldenring JR, Ham AJ, Coffey RJ. in Mol. Cell. Proteomics 2008, 7:1651-67 (PubMed).

The individual experiments show how well fairly straightforward proteomics techniques can perform on vesicular membrane proteins. They also demonstrate of the type of comprehensive results that can be obtained using a proteome sequence that is almost completely the result of genome annotation.

Data set of the week: (2010/05/23)
A Global Protein Kinase and Phosphatase Interaction Network in Yeast.

This data set contains 450 pull-down experiments obtained from S. cerevisiae. This work was transferred from TRANCHE via ProteomExchange and it was published by Ashton Breitkreutz, Hyungwon Choi, Jeffrey R. Sharom, Lorrie Boucher, Victor Neduva, Brett Larsen, Zhen-Yuan Lin, Bobby-Joe Breitkreutz, Chris Stark, Guomin Liu, Jessica Ahn, Danielle Dewar-Darch, Teresa Reguly, Xiaojing Tang, Ricardo Almeida, Zhaohui Steve Qin, Tony Pawson, Anne-Claude Gingras, Alexey I. Nesvizhskii, Mike Tyers Science 2010 328:1043-6.

Each of the individual results is annotated with the identity of the bait used in the pull-down experiment. L-A and L-BC virus proteins are present in some of the pull-downs. The group did a remarkably job at detecting phosphopeptides for a study that did not do any specific enrichment for these peptides.

Data set of the week: (2010/05/16)
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast.

This data set contains 505 LC/MS/MS runs obtained from S. cerevisiae diploid and haploid populations. This work was transferred from TRANCHE via ProteomExchange and it was published in de Godoy LM, Olsen JV, Cox J, Nielsen ML, Hubner NC, Fröhlich F, Walther TC, Mann M. Nature. 2008 455:1251-4. (PubMed).

The results give a good indication of the relative abundance and observability of yeast proteins in both haploid and diploid cells using either trypsin or endopeptidase LysC to generate peptides and SILAC labels to provide relative quantitation. The data also shows very good examples of the major proteins observable from the double stranded DNA viruses L-A and L-BC that are almost ubiquitously present in yeast cell cultures. In some cases, these proteins are very strongly observed (e.g. protein #3 in GPM77711001229) and the SILAC labelling can used to estimate the relative amounts of virus present in the two cell types. To located the virus and virus-related proteins in any of the individual runs, type "virus" into the Find box at the top of any model page (click here for an example).

Data set of the week: (2010/05/09)
Phosphoproteome analysis of Drosophila melanogaster embryo.

This data set contains 24 LC/MS/MS runs obtained from D. melanogaster embryos. This work was transferred from TRANCHE via ProteomExchange and it was published in Zhai B, Villén J, Beausoleil SA, Mintseris J, Gygi SP, J Proteome Res. 2008 7:1675-82 (PubMed).

The assignments in this data set give a good overview of phosphorylation in D. melanogaster and they are good examples of phosphopeptides identified using an Orbitrap-LTQ hybrid instrument with CID. The mapped phosphorylation sites from this data set were a major contribution to the pSYT annotation now available for the fruit fly. The predominance of yolk proteins and other larvae-specific proteins in the identified peptides gives a good view of the phosphorylation patterns on proteins that may be under-represented or absent from studies that use mature flies or cells from tissue culture.

Data set of the week: (2010/05/02)
Activated Macrophage Proteomics

This data set contains 9 merged results obtained from human macrophages under various conditions. This work was transferred from a TRANCHE project of the same name, created and maintained by Maureen M. Goodenow, Dept. of Pathology, Immunology and Laboratory Medicine University of Florida.

The experiments reported by Dr. Goodenow are proteomics survey studies of macrophages, in which the proteomes of treated cells are separated by SDS-PAGE and the resulting gel is sliced into 15 pieces. The proteins are then digested, the peptides extracted and run using LC/MS/MS. Each one of the entries in GPMDB correspond to the merged results of the 15 bands. They are good examples of what can be done using gel-slicing experiments to obtain proteomics information about a cell type. It is also an admirable example of valuable data being made available to the general community by an individual investigator.

Data set of the week: (2010/04/25)
Large-scale quantitative LC-MS/MS analysis of detergent-resistant membrane proteins from rat renal collecting duct.

This data set contains 78 LC/MS/MS runs obtained from membrance enriched fractions of tissue samples from rat renal ducts. It was originally published by Yu MJ, Pisitkun T, Wang G, Aranda JF, Gonzales PA, Tchapyjnikov D, Shen RF, Alonso MA, Knepper MA. in Am J Physiol Cell Physiol. 2008 295:C661-78 (PubMed). The data was transferred to GPMDB from TRANCHE via the ProteomExchange mechanism.

This study demonstrates that it is possible to generate very good results from membrane proteins isolated from tissue, even those that do not readily dissolve in detergent solutions, such as lipid raft proteins. GO analysis of the resulting protein identifications shows very significant enrichments in proteins known to be either integral membrane, membrane associated or part of the extracellular matrix.

Data set of the week: (2010/04/18)
Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins.

This data set contains 70 LC/MS/MS runs obtained using TAP-tag protein isolation, SDS-PAGE separation followed by tandem mass spectrometry. It was originally published by Fernández E, Collins MO, Uren RT, Kopanitsa MV, Komiyama NH, Croning MD, Zografos L, Armstrong JD, Choudhary JS, Grant SG. Mol Syst Biol. 2009;5:269 (PubMed). The data corresponds to the PeptideAtlas accession PAe001454 and was transferred to GPMDB via the ProteomExchange mechanism.

The results are a good demonstration of the depth and detail of a particular molecular system that can be obtained by coupling TAP-tagging with protein and subsequent peptide separations. The use of multiple gel slices allows a depth of proteome coverage that would be difficult to obtain using other techniques.

Data set of the week: (2010/04/11)
Proteomics of mouse liver microsomes

This data set contains 9 LC/MS/MS runs obtained using SDS-PAGE separation followed by tandem mass spectrometry. It was originally published by Zgoda VG, Moshkovskii SA, Ponomarenko EA, Andreewski TV, Kopylov AT, Tikhonova OV, Melnik SA, Lisitsa AV, and Archakov AI in Proteomics, 2009,9:4102-5 (PubMed). The data corresponds to the PRIDE accessions 8848-8856 and was transferred to GPMDB via the ProteomExchange mechanism.

This data set is an example of the isolation of a specific experimental fraction (mouse liver microsome from the endoplasmic reticulum) that provides a good representation of proteins not commonly observed, in this case the cytochrome P450 family of metabolic oxidases. The quality of the isolation can be easily seen when viewed as either KEGG pathways or GO cellular components.

Data set of the week: (2010/04/04)
Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations

This data set contains 369 LC/MS/MS runs obtained using a Thermo Finnigan LTQ instrument. It was originally published by Merrihew GE, Davis C, Ewing B, Williams G, Käll L, Frewen BE, Noble WS, Green P, Thomas JH, MacCoss MJ. in Genome Res. 2008, 18:1660-9 (PubMed). The data was obtained directly from the authors' web site and it is not currently held in any of the other ProteomExchange data sites.

The original analysis of this data set in the publication used the C. elegans WS150 proteome sequence and it was found to indicate the presence of additional coding sequences. The analysis in GPMDB was performed using the WS200 proteome (ENSEMBL v. 55), which has taken into account the original work. It serves as a good example of the proteins that can be seen using conventional proteomics techniques in C. elegans.

Data set of the week: (2010/03/28)
Global proteomic profiling of Shigella dysenteriae Sd1617

This data corresponds to Peptidome Study PSE140, comprised of samples PSM1302, PSM1303 and PSM1304 The data was obtained by Rembert Pieper, Srilatha Kuntumalla, Shih-Ting Huang at the J. Craig Venter Institute and it was transferred from Peptidome via ProteomExchange.

Each of the samples is composed of 3 replicate multidimensional chromatography runs of soluble proteins obtained from S. dysenteriae. The tandem mass spectra are good quality, obtained using a Thermo LTQ instrument. The results give a good indication of the type of depth and reproducibility that can be expected in this type of straight-forward analysis of soluble proteins from an enterobacterial culture.

Data set of the week: (2010/03/21)
Global Impact of Oncogenic Src on a Phosphotyrosine Proteome

The data is composed of 31 separate runs. The data was obtained from a study published in J. Proteome Res., 2008, 7 (8), pp 3447–3460, by Weifeng Luo, Robbert J. Slebos, Salisha Hill, Ming Li, Jan Brbek, Ramars Amanchy, Raghothama Chaerkady, Akhilesh Pandey, Amy-Joan L. Ham and Steven K. Hanks (DOI: 10.1021/pr800187n). This information was transferred from TRANCHE through ProteomExchange.

The data investigates the impact of Src transformation of mouse cells by determining the tyrosine phosphorylation differences between control and transformed cells. The data also demonstrates the utility of using multiple peptidases to increase the coverage of peptides, compared to trypsin alone. The data is very high quality LTQ data and it is an excellent reference work for what is to be expected when looking for mouse tyrosine phosphophorylation.

Data set of the week: (2010/03/14)
Quantitative phosphoproteomic analysis reveals vasopressin V2-receptor-dependent signaling pathways in renal collecting duct cells.

The data is composed of 2 separate sets, corresponding to the Peptidome accession numbers PSM1275 and PSM1276. The data was obtained from a study published in Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3882-7, by Rinschen MM, Yu MJ, Wang G, Boja ES, Hoffert JD, Pisitkun T, and Knepper MA (PubMed). This information was transferred from TRANCHE through ProteomExchange. The data is of high quality, containing good identifications of serine and threonine phosphorylation sites in M. musculus proteins and it is an excellent example of the use of SILAC to monitor the relative quantitation of protein phosphorylation.

Data set of the week: (2010/03/07)
Phosphorylation dynamics during early differentiation of human emrbyonic stem cells.

The data is composed of 12 individual LC/MS/MS runs obtained from a study published in Cell Stem Cell, Volume 5, Issue 2, 214-226, 7 August 2009 by Van Hoof D, Muñoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, and Krijgsveld J. (PubMed). This information was transferred from TRANCHE through ProteomExchange. Each of these data sets is large and contain significant numbers of phosphorylated peptides.

The experiments performed were to investigate how "pluripotent stem cells self-renew indefinitely and possess characteristic protein-protein networks that remodel during differentiation. How this occurs is poorly understood. Using quantitative mass spectrometry, the (phospho)proteome of human embryonic stem cells (hESCs) was analyzed during differentiation induced by bone morphogenetic protein (BMP) and removal of hESC growth factors."

Data set of the week: (2010/02/28)
A Lectin HPLC Method to Enrich Selectively-glycosylated Peptides from Complex Biological Samples.

The data is composed of 83 individual LC/MS/MS runs obtained from a study published in J Vis Exp. 2009 Oct 1;(32). pii: 1398 by Johansen E, Schilling B, Lerch M, Niles RK, Liu H, Li B, Allen S, Hall SC, Witkowska HE, Regnier FE, Gibson BW, Fisher SJ, and Drake PM (PubMed). This information was transferred from TRANCHE through ProteomExchange.

Briefly, plasma was depleted of the fourteen most abundant proteins using a multiple affinity removal system. Depleted plasma was trypsin-digested and separated into flow-through and bound fractions by SNA or AAL HPLC. The fractions were treated with PNGaseF to remove N-linked glycans, and analyzed by LC-MS/MS on a QStar Elite. There is an accompanying video explaining the methods used.

Data set of the week: (2010/02/21)
Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors.

The data is composed of 729 individual LC/MS/MS runs obtained from a study published in Nature Biotechnology by Bantscheff M, Eberhard D, Abraham Y, Bastuck S, Boesche M, Hobson S, Mathieson T, Perrin J, Raida M, Rau C, Reader V, Sweetman G, Bauer A, Bouwmeester T, Hopf C, Kruse U, Neubauer G, Ramsden N, Rick J, Kuster B, and Drewes G. (DOI: 10.1038/nbt1328). This information was transferred from PRIDE through ProteomExchange (PRIDE accession numbers 2445-3178).

Labelling with iTRAQ is used for quantitative profiling of the consequences of the introductions of tge drugs imatinib (Gleevec), dasatinib (Sprycel) and bosutinib in K562 cells confirms known targets including ABL and SRC family kinases.

Data set of the week: (2010/02/14)
Cell-Specific Information Processing in Segregating Populations of Eph Receptor Ephrin-Expressing Cells.

This dataset was transfered to GPMDB via ProteoExchange from PRIDE. The data is composed of 2 large LC/MS/MS runs is from a study published in Science by Jørgensen C, Sherman A, Chen GI, Pasculescu A, Poliakov A, Hsiung M, Larsen B, Wilkinson DG, Linding R, and Pawson T (DOI: 10.1126/science.1176615).

The data is from a set of quantitative mass spectrometric analyses of mixed populations of EphB2- and ephrin-B1–expressing cells that were labeled with different isotopes revealed cell-specific tyrosine phosphorylation events. The data is of very high quality and it has a very rich set of tyrosine phosphorylated peptides.

Data set of the week: (2010/02/07)
The value of using multiple proteases for large-scale mass spectrometry-based proteomics.

This dataset was transfered to GPMDB via ProteoExchange from TRANCHE. The data is composed of 15 LC/MS/MS runs is from a study published in J. Proteome Research by Danielle L. Swaney, Craig D. Wenger and Joshua J. Coon (DOI: 10.1021/pr900863u).

The data is from experiments in which an S. cerevisiae whole cell lysate was digested with one of five enzymes (trypsin, LysC, ArgC, AspN, and GluC), in triplicate. The results clearly show that any of these proteases can be used very effectively with standard proteomics equipment, giving very similar protein identifications.

Data set of the week: (2010/01/31)
Identifying blood biomarkers and physiological processes that distinguish humans with superior performance under psychological stress.

This dataset was transfered to GPMDB via ProteoExchange from PRIDE (Pride accessions 10075-10092). The data (GPM77710000113-GPM77710000130) is from a study published in PLoS One by Cooksey AM, Momen N, Stocker R, and Burgess SC (PLoS One. 2009 Dec 18;4(12):e8371 PubMed).

The results show the plasma proteins that change in response to the Modular Egress Training psychological stress test, given to a group of naval aviation students. The data was obtained using an LCQ DECA XP Plus and analyzed using X! Hunter (annotated spectrum library searches).

Data set of the week: (2010/01/24)
High quality catalog of proteotypic peptides from human heart

This dataset was transfered to GPMDB from the authors' web site, corresponding to the manuscript of the same name, Kline, KG, et al.,J Proteome Res. 2008 Nov;7(11):5055-61. PubMed. This data is not currently available on other ProteomExchange respositories.

The data consists of 96 LCMS runs analyzed with a ThermoFinnigan LTQ mass spectrometer. It is a good example of the type of data that can be obtained from cardiac muscle using multidimensional chromatography directly on tissue lysate.

Data set of the week: (2010/01/17)
A Mitochondrial Protein Compendium Elucidates Complex I Disease Biology

This dataset was transfered to GPMDB from TRANCHE, corresponding to the manuscript of the same name, Pagliarini, DJ, et al., Cell 134:112-123 doi:10.1016/j.cell.2008.06.016.

The data consists of 26 individual data sets, composed of replicates of mitochondrial proteins obtained from a variety of mouse tissues (cerebellum, cerebrum, brainstem, spinal cord, kidney, liver, heart, skeletal muscle, testis and placenta). It is a good example of high quality proteomics data, obtained using a Thermo-Finnigan Orbitrap hybrid mass spectrometer.

Data set of the week: (2010/01/10)
Comparative analysis of the human and mouse placental transcriptome and proteome

This dataset was transfered to GPMDB from Peptidome via ProteoExchange, from the Peptidome entries PSM1063 (mouse) and and PSM1064 (human). The cells in the tissue were separated from extracellular proteins and various subcellular fractions were analyzed separately. The data was originally published in Cox B, et al., Mol Syst Biol 2009;5:279. PMID: 19536202.

Note: the Peptidome entry misidentifies the mass spectrometry platform as being an "TRAP-FTMS" while it is actually a Thermo-Finnigan LTQ (with no additional hybrid component).

Data set of the week: (2010/01/03)
Large-scale phosphorylation analysis of mouse liver

This dataset was transfered to GPMDB from TRANCHE and it is not currently held in any other ProteoExchange database (see data). It is credited to Villén J, Beausoleil SA, Gerber SA, and Gygi SP, and it is described in Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1488-93.

This data set is a good example of the quality of phosphorylation data that can be obtained using SCX separation of a tissue extract, followed by IMAC phosphopeptide enrichment of each fraction, when using an LTQ-Orbitrap mass spectrometer. The data view that is obtained from the link above shows all of the detected phosphopeptides, with a peptide false positive rate of ~ 0.14%, i.e., about 10 times more stringent than the analysis in the original paper.

Data set of the week: (2009/12/28)
Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

This dataset was transfered to GPMDB via ProteoExchange from PRIDE (see data). It is credited to Delmotte N, et al. and it is described in Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16428-33.

Data-set-of-the-week is a new feature for GPMDB, started with the intent of highlighting high quality data sets that have been made available via GPMDB and ProteomExchange. Data sets will be selected by a panel, but any suggestions (email to dsotw@thegpm.org) of suitable data will be considered.

Click here to check the news archive.

Copyright © 2008, The Global Proteome Machine Organization

Privacy Statement