Guidelines for reporting the use of mass spectrometry in proteomics

Taylor, Chris; Binz, Pierre‐Alain; Aebersold, Ruedi; Affolter, Michael; Barkovich, Robert; Deutsch, Eric W.; Horn, David M.; Hühmer, Andreas; Kussmann, Martin; Lilley, Kathryn S.; Macht, Marcus; Mann, Matthias; Müller, Dieter; Neubert, Thomas A.; Nickson, Janice; Patterson, Scott D.; Raso, Roberto; Resing, Kathryn; Seymour, Sean L.; Tsugita, Akira; Xenarios, Ioannis; Zeng, Rong; Julian, Randall K.

doi:10.1038/nbt0808-860

Cited by 76 publications

(39 citation statements)

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“…Search results were assessed and combined in Proteinscape 3.1 (Bruker Daltonics, Bremen, Germany). To comply with MIAPE (Minimum Information About a Proteomics Experiment) guidelines (Taylor et al, 2007;Binz et al, 2008;Taylor et al, 2008), search parameters, line spectra, quality control criteria and identifications were deposited in the PRIDE repository and can be accessed using PRIDE Inspector (accession numbers 28622-28631) Csordas et al, 2012;Wang et al, 2012;Csordas et al, 2013;Vizcaíno et al, 2013). MS molecular features identified with DataAnalysis 4.0 were imported into ProfileAnalysis 2.0 (both Bruker Daltonics) and comparison of peptide abundances in treated versus control samples was performed by quantitation of chromatographic peak area integrals of peptides with matching retention time (Rt) and mass over charge ratio (m/z).…”

Section: Label-free Quantitative Proteome Profile Analysismentioning

confidence: 99%

Salinity-induced activation of the myo-inositol biosynthesis pathway in tilapia gill epithelium

Sacchi

Villarreal

et al. 2013

Journal of Experimental Biology

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SUMMARYThe myo-inositol biosynthesis (MIB) pathway converts glucose-6-phosphate to the compatible osmolyte myo-inositol that protects cells from osmotic stress. Using proteomics, the enzymes that constitute the MIB pathway, myo-inositol phosphate synthase (MIPS) and inositol monophosphatase 1 (IMPA1), are identified in tilapia (Oreochromis mossambicus) gill epithelium. Targeted, quantitative, label-free proteomics reveals that they are both upregulated during salinity stress. Upregulation is stronger when fish are exposed to severe (34 ppt acute and 90 ppt gradual) relative to moderate (70 ppt gradual) salinity stress. IMPA1 always responds more strongly than MIPS, suggesting that MIPS is more stable during salinity stress. MIPS is N-terminally acetylated and the corresponding peptide increases proportionally to MIPS protein, while non-acetylated N-terminal peptide is not detectable, indicating that MIPS acetylation is constitutive and may serve to stabilize the protein. Hyperosmotic induction of MIPS and IMPA1 is confirmed using western blot and real-time qPCR and is much higher at the mRNA than at the protein level. Two distinct MIPS mRNA variants are expressed in the gill, but one is more strongly regulated by salinity than the other. A single MIPS gene is encoded in the tilapia genome whereas the zebrafish genome lacks MIPS entirely. The genome of euryhaline tilapia contains four IMPA genes, two of which are expressed, but only one is salinity regulated in gill epithelium. The genome of stenohaline zebrafish contains a single IMPA gene. We conclude that the MIB pathway represents a major salinity stress coping mechanism that is regulated at multiple levels in euryhaline fish but absent in stenohaline zebrafish.Supplementary material available online at http://jeb.biologists.org/lookup/suppl

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Section: Label-free Quantitative Proteome Profile Analysismentioning

confidence: 99%

Salinity-induced activation of the myo-inositol biosynthesis pathway in tilapia gill epithelium

Sacchi

Villarreal

et al. 2013

Journal of Experimental Biology

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“…Additional fields and tables are easily added to any mzResults file; these can be used to provide metadata in support of the MIAPE standard (10,19) or other results such as consensus scoring from multiple peptide search algorithms. As noted above, SQLite is widely supported with libraries available for many commonly used programming languages, allowing researchers to view, use, and modify mzResults files in their preferred programming environment.…”

Section: Methodsmentioning

confidence: 99%

mzResults: An Interactive Viewer for Interrogation and Distribution of Proteomics Results

Webber

Askenazi

Marto

2011

Molecular & Cellular Proteomics

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The growing use of mass spectrometry in the context of biomedical research has been accompanied by an increased demand for distribution of results in a format that facilitates rapid and efficient validation of claims by reviewers and other interested parties. However, the continued evolution of mass spectrometry hardware, sample preparation methods, and peptide identification algorithms complicates standardization and creates hurdles related to compliance with journal submission requirements. Moreover, the recently announced Philadelphia Guidelines (1, 2) suggest that authors provide native mass spectrometry data files in support of their peer-reviewed research articles. These trends highlight the need for data viewers and other tools that work independently of manufacturers' proprietary data systems and seamlessly connect proteomics results with original data files to support user-driven data validation and review. Based upon our recently described API 1 -based framework for mass spectrometry data analysis (3, 4), we created an interactive viewer (mzResults) that is built on established database standards and enables efficient distribution and interrogation of results associated with proteomics experiments, while also providing a convenient mechanism for authors to comply with data submission standards as described in the Philadelphia Guidelines. In addition, the architecture of mzResults supports in-depth queries of the native mass spectrometry files through our multiplierz software environment. We use phosphoproteomics data to illustrate the features and capabilities of mzResults. Molecular & Cellular Proteomics 10: 10.1074/mcp.M110.003970, 1-7, 2011.Burgeoning demand for systematic generation of mass spectrometry data in support of biomedical studies continues to drive the development of proteomics technologies at a rapid pace. The concomitant expansion of proteomics data that accompany scientific reports, often as supplementary materials, has catalyzed numerous and somewhat disparate efforts to standardize results reporting (5-11). However, as an emerging field of endeavor, proteomics faces a unique set of challenges that complicate efforts to establish open and portable formats for sharing results; specific obstacles include:(i) Technology innovation: mass spectrometry in particular continues to evolve rapidly, leading to multiple hardware configurations, scan functions, and proprietary file formats.(ii) Discovery mode experiments: the majority of studies are performed in discovery mode with the goal of maximizing new information about the protein content of each sample. As a result, methods are in a state of flux with correspondingly little standardization.(iii) Unbounded measurement space: genetic alterations (alternate splicing, translocations, etc.) and post-translational processing (modifications, enzymatic cleavage, etc.) significantly amplify the number of chemically distinct protein products relative to that predicted by the genetic code. As a result, a large fraction of MS/MS spectra go unassigned...

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“…Furthermore, as the immunopeptidomics MS approach and the supportive bioinformatics tools are those commonly used in general proteomics techniques, several parts of the guidelines below overlap with the existing general MIAPE guidelines,10, 11, 12, 13 developed under the umbrella of the HUPO Proteomics Standards Initiative, and the Paris Guidelines on reporting and deposition of proteomics datasets (http://www.mcponline.org/site/misc/ParisReport_Final.xhtml). For the sake of completeness and clarity, we have included overlapping content and elaborate further on the immunopeptidomics specific aspects.…”

Section: Introductionmentioning

confidence: 99%

Minimal Information About an Immuno‐Peptidomics Experiment (MIAIPE)

Lill¹,

Veelen

Admon

et al. 2018

Proteomics

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Minimal information about an immuno‐peptidomics experiment (MIAIPE) is an initiative of the members of the Human Immuno‐Peptidome Project (HIPP), an international program organized by the Human Proteome Organization (HUPO). The aim of the MIAIPE guidelines is to deliver technical guidelines representing the minimal information required to sufficiently support the evaluation and interpretation of immunopeptidomics experiments. The MIAIPE document has been designed to report essential information about sample preparation, mass spectrometric measurement, and associated mass spectrometry (MS)‐related bioinformatics aspects that are unique to immunopeptidomics and may not be covered by the general proteomics MIAPE (minimal information about a proteomics experiment) guidelines.

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Guidelines for reporting the use of mass spectrometry in proteomics

Cited by 76 publications

References 1 publication

Salinity-induced activation of the myo-inositol biosynthesis pathway in tilapia gill epithelium

Salinity-induced activation of the myo-inositol biosynthesis pathway in tilapia gill epithelium

mzResults: An Interactive Viewer for Interrogation and Distribution of Proteomics Results

Minimal Information About an Immuno‐Peptidomics Experiment (MIAIPE)

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