A data repository for proteomic data sets. The ProteomeExchange consortium, as a whole, aims to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories, as well as to encourage optimal data dissemination. ProteomeXchange provides access to a number of public databases, and users can access and submit data sets to the consortium's PRIDE database and PASSEL/PeptideAtlas.

The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination.

The cerebrospinal fluid (CSF) proteome data set presented herein was obtained after immunodepletion of abundant proteins and off-gel electrophoresis fractionation of a commercial pool of normal human CSF; liquid chromatography tandem mass spectrometry analysis was performed with a linear ion trap-Orbitrap Elite. We report the identification of 12 344 peptides mapping on 2281 proteins. In the context of the Chromosome-centric Human Proteome Project (C-HPP), the existence of seven missing proteins is proposed to be validated. This data set is available to the ProteomeXchange Consortium (http://www.proteomexchange.org/) with the data set identifier PXD008029.

In the context of bacterial infections, it is imperative that physiological responses can be studied in an integrated manner, meaning a simultaneous analysis of both the host and the pathogen responses. To improve the sensitivity of detection, data-independent acquisition (DIA)-based proteomics was found to outperform data-dependent acquisition (DDA) workflows in identifying and quantifying low-abundant proteins. Here, by making use of representative bacterial pathogen/host proteome samples, we report an optimized hybrid library generation workflow for DIA mass spectrometry relying on the use of data-dependent and in silico-predicted spectral libraries. When compared to searching DDA experiment-specific libraries only, the use of hybrid libraries significantly improved peptide detection to an extent suggesting that infection-relevant host-pathogen conditions could be profiled in sufficient depth without the need of a priori bacterial pathogen enrichment when studying the bacterial proteome. Proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD017904 and PXD017945.

This article contains consolidated proteomic data obtained from xylem sap collected from tomato plants grown in Fe- and Mn-sufficient control, as well as Fe-deficient and Mn-deficient conditions. Data presented here cover proteins identified and quantified by shotgun proteomics and Progenesis LC-MS analyses: proteins identified with at least two peptides and showing changes statistically significant (ANOVA; p ≤ 0.05) and above a biologically relevant selected threshold (fold ≥ 2) between treatments are listed. The comparison between Fe-deficient, Mn-deficient and control xylem sap samples using a multivariate statistical data analysis (Principal Component Analysis, PCA) is also included. Data included in this article are discussed in depth in "Effects of Fe and Mn deficiencies on the protein profiles of tomato (Solanum lycopersicum) xylem sap as revealed by shotgun analyses", Ceballos-Laita et al., J. Proteomics, 2018. This dataset is made available to support the cited study as well to extend analyses at a later stage. Resources in this dataset:Resource Title: ProteomeExchange submission PXD007517. Xylem sap shotgun proteomics from Fe- and Mn-deficient and Mn-toxic tomato plants. . File Name: Web Page, url: http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD007517 The MS proteomics data have been deposited to the ProteomeXchange Consortium via the Pride partner repository with the data set identifier PXD007517. Also includes FTP location. Files available at https://www.ebi.ac.uk/pride/archive/projects/PXD007517 via HTML, FTP, or Fast (Aspera) download : 1 SEARCH.xml file, 1 Peak file, 24 RAW files, 1 Mascot information.xlsx file. Supplementary data associated with this article can be found in the online version at http://dx.doi.org/10.1016/j.dib.2018.01.034

The mass spectrometry proteomics data files have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the data set identifier PXD013243 and title "Morphological plasticity in a sulfur-oxidizing bacterium from the SUP05 clade enhances dark carbon fixation"
(see https://www.ebi.ac.uk/pride/archive/projects/PXD013243).

These data were published in Shah et al. (2019).

Milk-derived exosomes have been reported, which are involved in many biological processes. The exosomes derived from mammary glands are not known yet, and their relationship with mammary gland lactation and the origin of milk-derived exosomes are largely unclear. The present study aimed to investigate the proteome of exosomes derived from bovine mammary epithelial cells (BMECs) and compare them with milk-derived exosomes in the database. BMEC-derived exosomes were successfully separated from the culture supernatant of BMECs by a combined ultracentrifugation approach, and the purity of exosomes was identified by western blot analysis. Liquid chromatography with tandem mass spectrometry identified 638 proteins in BMEC-derived exosomes. The MS data were deposited into the PUBLIC repository ProteomeXchange, dataset identifier(s): https://www.iprox.org/page/PSV023.html;?url=1590961453176tKpa. Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that these proteins were associated with specific biological processes and molecular functions of metabolism. Cross comparison of these proteins with the protein database of milk exosomes showed that 77 common expressed proteins (CEPs) were in both BMEC- and milk-derived exosomes. The KEGG pathway analysis for these CEPs showed that they were mainly involved in signaling pathways associated with milk biosynthesis in BMECs. Among these CEPs, six proteins have been previously reported to be associated with the lactation function. The western blot analysis detected that expression of these six proteins in BMEC-derived exosomes was increased after the stimulation of methionine and β-estradiol on BMECs. In summary, the proteome of BMEC-derived exosomes reveals that they are associated with milk biosynthesis in BMECs and might be a source of milk-derived exosomes.

Protein-Protein, Genetic, and Chemical Interactions for Truman AW (2015):The quantitative changes in the yeast Hsp70 and Hsp90 interactomes upon DNA damage. curated by BioGRID (https://thebiogrid.org); ABSTRACT: The molecular chaperones Hsp70 and Hsp90 participate in many important cellular processes, including how cells respond to DNA damage. Here we show the results of applied quantitative affinity-purification mass spectrometry (AP-MS) proteomics to understand the protein network through which Hsp70 and Hsp90 exert their effects on the DNA damage response (DDR). We characterized the interactomes of the yeast Hsp70 isoform Ssa1 and Hsp90 isoform Hsp82 before and after exposure to methyl methanesulfonate. We identified 256 chaperone interactors, 146 of which are novel. Although the majority of chaperone interaction remained constant under DNA damage, 5 proteins (Coq5, Ast1, Cys3, Ydr210c and Rnr4) increased in interaction with Ssa1 and/or Hsp82. This data presented here are related to 1. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaino et al. (2013) [2]) with the dataset identifier PXD001284.

Data to accompany figure S2Proteomics of FRC-derived matricesIn vitro FRC cell line-derived matrices generated after 5 days in culture were subjected to proteomic analysis by mass spectrometry. Summary data in xls spreadsheet. SWATH dataset uploaded to PRIDE repository ID=PXD015816http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD015816AbstractLymph nodes (LNs) work as filtering organs, constantly sampling peripheral cues. This is facilitated by the conduit network, a parenchymal tubular-like structure formed of bundles of aligned extracellular matrix (ECM) fibrils ensheathed by fibroblastic reticular cells (FRCs). LNs undergo 5-fold expansion with every adaptive immune response and yet these ECM-rich structures are not permanently damaged. Whether conduit integrity and filtering functions are affected during cycles of LN expansion and resolution is not known. Here we show that the conduit structure is disrupted during acute LN expansion but FRC-FRC contacts remain intact. In homeostasis, polarised FRCs adhere to the underlying substrate to deposit ECM ba-solaterally. ECM production by FRCs is regulated by the C-type lectin CLEC-2, expressed by dendritic cells (DCs), at transcriptional and secretory levels. Inflamed LNs maintain conduit size-exclusion, but flow becomes leaky, which allows soluble antigens to reach more antigen-presenting cells. We show how dynamic communication between peripheral tissues and LNs changes during immune responses, and describe a mechanism that enables LNs to prevent inflammation-induced fibrosis.HighlightsFRCs use polarized microtubule networks to guide matrix depositionCLEC-2/PDPN controls matrix production at transcriptional and post-transcriptional levelsFRCs halt matrix production and decouple from conduits during acute LN expansionConduits leak soluble antigen during acute LN expansion

p63 is an important regulator of epithelial development expressed in different variants containing (TA) or lacking (ΔN) the N-terminal transactivation domain. The different isoforms regulate stem-cell renewal and differentiation as well as cell senescence. Several studies indicate that p63 isoforms also play a role in cancer development; however, very little is known about the role played by p63 in regulating the cancer stem phenotype. Here we investigate the cellular signals regulated by TAp63 and ΔNp63 in a model of epithelial cancer stem cells. To this end, we used colon cancer stem cells, overexpressing either TAp63 or ΔNp63 isoforms, to carry out a proteomic study by chemical-labeling approach coupled to network analysis. Our results indicate that p63 is implicated in a wide range of biological processes, including metabolism. This was further investigated by a targeted strategy at both protein and metabolite levels. The overall data show that TAp63 overexpressing cells are more glycolytic-active than ΔNp63 cells, indicating that the two isoforms may regulate the key steps of glycolysis in an opposite manner. The mass-spectrometry proteomics data of the study have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with data set identifiers PXD000769 and PXD000768.

This dataset is a label-free quantitation of proteins milk and dry secretions from the end of lactation through day 21 of the dry period using liquid chromatography with tandem mass spectrometry (LC-MS/MS). The data supplied in this article supports the accompanying publication entitled “Characterization of bovine mammary gland dry secretions and their proteome from the end of lactation through day 21 of the dry period”. The Thermo mass spectrometry raw files and MaxQuant files have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset number PXD017837. Resources in this dataset:Resource Title: Characterization of Bovine Dry Secretions and their Proteome from the End of Lactation Through Day 21 of the Dry Period - ProteomeXchange Consortium via the PRIDE partner repository, Project PXD017837. File Name: Web Page, url: https://www.ebi.ac.uk/pride/archive/projects/PXD017837 Thermo raw file code for Pride raw files and supplemental Excel files. The 3 technical replicates are denoted as a letter A, B and C. The number following is the cow identification number for 11 cows used. The final two-digit number after the underscore is the day sampled where _01 = day 1, _03 = day 3, _10 = day 10 and _21 = day 21 of dry period. For example, A1313_01 is technical replicate A for cow 1313 collected on day 1. B1313_03 is technical replicate B for cow 1313 collected on day 3. Details of sample and data processing protocols are provided.

For the C-HPP consortium, dark proteins include not only uPE1, but also missing proteins (MPs, PE2–4), smORFs, proteins from lncRNAs, and products from uncharacterized transcripts. Here, we investigated the expression of dark proteins in the human testis by combining public mRNA and protein expression data for several tissues and performing LC–MS/MS analysis of testis protein extracts. Most uncharacterized proteins are highly expressed in the testis. Thirty could be identified in our data set, of which two were selected for further analyses: (1) A0AOU1RQG5, a putative cancer/testis antigen specifically expressed in the testis, where it accumulates in the cytoplasm of elongated spermatids; and (2) PNMA6E, which is enriched in the testis, where it is found in the germ cell nuclei during most stages of spermatogenesis. Both proteins are coded on Chromosome X. Finally, we studied the expression of other dark proteins, uPE1 and MPs, in a series of human tissues. Most were highly expressed in the testis at both the mRNA and protein levels. The testis appears to be a relevant organ to study the dark proteome, which may have a function related to spermatogenesis and germ cell differentiation. The mass spectrometry proteomics data have been deposited with the ProteomeXchange Consortium under the data set identifier PXD009598.

Protein-Protein, Genetic, and Chemical Interactions for Wolfgeher D (2015):The dynamic interactome of human Aha1 upon Y223 phosphorylation. curated by BioGRID (https://thebiogrid.org); ABSTRACT: Heat Shock Protein 90 (Hsp90) is an essential chaperone that supports the function of a wide range of signaling molecules. Hsp90 binds to a suite of co-chaperone proteins that regulate Hsp90 function through alteration of intrinsic ATPase activity. Several studies have determined Aha1 to be an important co-chaperone whose binding to Hsp90 is modulated by phosphorylation, acetylation and SUMOylation of Hsp90 [1], [2]. In this study, we applied quantitative affinity-purification mass spectrometry (AP-MS) proteomics to understand how phosphorylation of hAha1 at Y223 altered global client/co-chaperone interaction [3]. Specifically, we characterized and compared the interactomes of Aha1-Y223F (phospho-mutant form) and Aha1-Y223E (phospho-mimic form). We identified 99 statistically significant interactors of hAha1, a high proportion of which (84%) demonstrated preferential binding to the phospho-mimic form of hAha1. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.

The dataset includes total spectral counts for proteins and peptides. Four files and a link to raw data at the domain repository are included:

1) Sample metadata file with station locations, depth, time of collection and sample IDs described by this BCO-DMO page. (original file name: DeepDOM_sample_metadata_for_OPP.csv)

2) Raw mass spectral data files are available on PRIDE and ProteomeXchange:

ProteomeXchange title: Microbial Metaproteome from the Western Atlantic Ocean DeepDOM KN210-04 Expedition

ProteomeXchange accession: PXD034035

Project Webpage: http://www.ebi.ac.uk/pride/archive/projects/PXD034035

FTP Download: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/05/PXD034035

Mass spectrometry analysis (data-independent acquisition) derived intensities are reported here for all breast tumor samples (n = 75). RAW data files for these samples are accessible via ProteomeXchange with the dataset identifiers PXD032266 (S samples) and PXD037428 (V samples). Protein intensities were Log2 transformed and scaled (samples and proteins).

This dataset was used for Figure 5 in the following manuscript: "Proteogenomics decodes the evolution of human ipsilateral breast cancer". De Marchi T, Pyl PT, Sjöström M, Reinsbach SE, DiLorenzo S, Nystedt B, Tran L, Pekar G, Wärnberg F, Fredriksson I, Malmström P, Fernö M, Malmström L, Malmström J, Nimèus E. accepted for publication

Integrated proteome resources center in China to accelerate data sharing in proteomics. Composed of data submission system and proteome database. Submission system is established under the guidance of data-sharing policy made by ProteomeXchange consortium. Registered users can submit their proteomic datasets to iProX in public or private modes. Once associated manuscript has been published, dataset becomes automatically public.

Kinase enrichment utilizing broad-spectrum kinase inhibitors enables the identification of large proportions of the expressed kinome by mass spectrometry. However, the existing inhibitors are still inadequate in covering the entire kinome. Here, we identified a novel bisanilino pyrimidine, CTx-0294885, exhibiting inhibitory activity against a broad range of kinases in vitro, and further developed it into a Sepharose-supported kinase capture reagent. Use of a quantitative proteomics approach confirmed the selectivity of CTx-0294885-bound beads for kinase enrichment. Large-scale CTx-0294885-based affinity purification followed by LC–MS/MS led to the identification of 235 protein kinases from MDA-MB-231 cells, including all members of the AKT family that had not been previously detected by other broad-spectrum kinase inhibitors. Addition of CTx-0294885 to a mixture of three kinase inhibitors commonly used for kinase-enrichment increased the number of kinase identifications to 261, representing the largest kinome coverage from a single cell line reported to date. Coupling phosphopeptide enrichment with affinity purification using the four inhibitors enabled the identification of 799 high-confidence phosphosites on 183 kinases, ∼10% of which were localized to the activation loop, and included previously unreported phosphosites on BMP2K, MELK, HIPK2, and PRKDC. Therefore, CTx-0294885 represents a powerful new reagent for analysis of kinome signaling networks that may facilitate development of targeted therapeutic strategies. Proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the data set identifier PXD000239.

Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE)

Availability and implementation

The software is available on Github (https://github.com/CMRI-ProCan/CRANE). The datasets were obtained from ProteomeXchange (Identifiers—PXD002952 and PXD008651). Preliminary data and intermediate files are available via ProteomeXchange (Identifiers—PXD020529 and PXD025103).

A suboptimal blood vitamin C (ascorbate) level increases the risk of several chronic diseases. However, the detection of hypovitaminosis C is not a simple task, as ascorbate is unstable in blood samples. In this study, we examined the serum proteome of mice lacking the gulonolactone oxidase (Gulo) required for the ascorbate biosynthesis. Gulo–/– mice were supplemented with different concentrations of ascorbate in drinking water, and serum was collected to identify proteins correlating with serum ascorbate levels using an unbiased label-free liquid chromatography-tandem mass spectrometry global quantitative proteomic approach. Parallel reaction monitoring was performed to validate the correlations. We uncovered that the serum proteome profiles differ significantly between male and female mice. Also, unlike Gulo–/– males, a four-week ascorbate treatment did not entirely re-establish the serum proteome profile of ascorbate-deficient Gulo–/– females to the optimal profile exhibited by Gulo–/– females that never experienced an ascorbate deficiency. Finally, the serum proteins involved in retinoid metabolism, cholesterol, and lipid transport were similarly affected by ascorbate levels in males and females. In contrast, the proteins regulating serum peptidases and the protein of the acute phase response were different between males and females. These proteins are potential biomarkers correlating with blood ascorbate levels and require further study in standard clinical settings. The complete proteomics data set generated in this study has been deposited to the public repository ProteomeXchange with the data set identifier: PXD027019.