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Article ; Online: SpectiCal:

Zhang, Nathan H / Deutsch, Eric W

2024 Volume 23, Issue 4, Page(s) 1519–1530

Abstract: Most tandem mass spectrometry fragmentation spectra have small calibration errors that can lead to suboptimal interpretation and annotation. We developed SpectiCal, a software tool that can read mzML files from data-dependent acquisition proteomics ... ...

Abstract	Most tandem mass spectrometry fragmentation spectra have small calibration errors that can lead to suboptimal interpretation and annotation. We developed SpectiCal, a software tool that can read mzML files from data-dependent acquisition proteomics experiments in parallel, compute
MeSH term(s)	Calibration ; Peptides/analysis ; Software ; Tandem Mass Spectrometry/methods ; Ions
Chemical Substances	Peptides ; Ions
Language	English
Publishing date	2024-03-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00882
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Article ; Online: Does the Ubiquitination Degradation Pathway Really Reach inside of the Chloroplast? A Re-Evaluation of Mass Spectrometry-Based Assignments of Ubiquitination.

van Wijk, Klaas J / Leppert, Tami / Sun, Zhi / Deutsch, Eric W

Journal of proteome research

2023 Volume 22, Issue 6, Page(s) 2079–2091

Abstract: A recent paper in Science Advances by Sun et al. claims that intra-chloroplast proteins in the model plant Arabidopsis can be polyubiquitinated and then extracted into the cytosol for subsequent degradation by the proteasome. Most of this conclusion ... ...

Abstract	A recent paper in Science Advances by Sun et al. claims that intra-chloroplast proteins in the model plant Arabidopsis can be polyubiquitinated and then extracted into the cytosol for subsequent degradation by the proteasome. Most of this conclusion hinges on several sets of mass spectrometry (MS) data. If the proposed results and conclusion are true, this would be a major change in the proteolysis/proteostasis field, breaking the long-standing dogma that there are no polyubiquitination mechanisms within chloroplast organelles (nor in mitochondria). Given its importance, we reanalyzed their raw MS data using both open and closed sequence database searches and encountered many issues not only with the results but also discrepancies between stated methods (e.g., use of alkylating agent iodoacetamide (IAA)) and observed mass modifications. Although there is likely enrichment of ubiquitination signatures in a subset of the data (probably from ubiquitination in the cytosol), we show that runaway alkylation with IAA caused extensive artifactual modifications of N termini and lysines to the point that a large fraction of the desired ubiquitination signatures is indistinguishable from artifactual acetamide signatures, and thus, no intra-chloroplast polyubiquitination conclusions can be drawn from these data. We provide recommendations on how to avoid such perils in future work.
MeSH term(s)	Ubiquitination ; Proteolysis ; Chloroplasts/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Arabidopsis/metabolism ; Mass Spectrometry
Chemical Substances	Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2023-04-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00178
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Article ; Online: Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future.

Jones, Andrew R / Deutsch, Eric W / Vizcaíno, Juan Antonio

Proteomics

2022 Volume 23, Issue 7-8, Page(s) e2200014

Abstract: Data independent acquisition (DIA) proteomics techniques have matured enormously in recent years, thanks to multiple technical developments in, for example, instrumentation and data analysis approaches. However, there are many improvements that are still ...

Abstract	Data independent acquisition (DIA) proteomics techniques have matured enormously in recent years, thanks to multiple technical developments in, for example, instrumentation and data analysis approaches. However, there are many improvements that are still possible for DIA data in the area of the FAIR (Findability, Accessibility, Interoperability and Reusability) data principles. These include more tailored data sharing practices and open data standards since public databases and data standards for proteomics were mostly designed with DDA data in mind. Here we first describe the current state of the art in the context of FAIR data for proteomics in general, and for DIA approaches in particular. For improving the current situation for DIA data, we make the following recommendations for the future: (i) development of an open data standard for spectral libraries; (ii) make mandatory the availability of the spectral libraries used in DIA experiments in ProteomeXchange resources; (iii) improve the support for DIA data in the data standards developed by the Proteomics Standards Initiative; and (iv) improve the support for DIA datasets in ProteomeXchange resources, including more tailored metadata requirements.
MeSH term(s)	Proteomics/methods ; Proteome ; Mass Spectrometry/methods ; Computational Biology/methods
Chemical Substances	Proteome
Language	English
Publishing date	2022-09-13
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202200014
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Article ; Online: Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format.

Eng, Jimmy K / Deutsch, Eric W

Proteomics

2020 Volume 20, Issue 21-22, Page(s) e1900362

Abstract: Protein identification by tandem mass spectrometry sequence database searching is a standard practice in many proteomics laboratories. The de facto standard for the representation of sequence databases used as input to sequence database search tools is ... ...

Abstract	Protein identification by tandem mass spectrometry sequence database searching is a standard practice in many proteomics laboratories. The de facto standard for the representation of sequence databases used as input to sequence database search tools is the FASTA format. The Human Proteome Organization's Proteomics Standards Initiative has developed an extension to the FASTA format termed the proteomics standards initiative extended FASTA format or PSI extended FASTA format (PEFF) where additional information such as structural annotations are encoded in the protein description lines. Comet has been extended to automatically analyze the post translational modifications and amino acid substitutions encoded in PEFF databases. Comet's PEFF implementation and example analysis results searching a HEK293 dataset against the neXtProt PEFF database are presented.
MeSH term(s)	Amino Acids ; Databases, Protein ; HEK293 Cells ; Humans ; Protein Processing, Post-Translational ; Proteome ; Proteomics ; Software
Chemical Substances	Amino Acids ; Proteome
Language	English
Publishing date	2020-04-02
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.201900362
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Article ; Online: Is the writing on the wall? The relationship between the number of disease-modifying anti-inflammatory bowel disease drugs used and the risk of surgical resection.

Mankarious, Marc M / Greene, Alicia C / Schaefer, Eric W / Clarke, Kofi / Kulaylat, Afif N / Jeganathan, Nimalan A / Deutsch, Michael J / Kulaylat, Audrey S

Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract

2024

Abstract: Background: Disease-modifying anti-inflammatory bowel disease drugs (DMAIDs) revolutionized the management of ulcerative colitis (UC). This study assessed the relationship between the number and timing of drugs used to treat UC and the risk of colectomy ...

Abstract	Background: Disease-modifying anti-inflammatory bowel disease drugs (DMAIDs) revolutionized the management of ulcerative colitis (UC). This study assessed the relationship between the number and timing of drugs used to treat UC and the risk of colectomy and postoperative complications. Methods: This was a retrospective review of adult patients with UC treated with disease-modifying drugs between 2005 and 2020 in the MarketScan database. Landmark and time-varying regression analyses were used to analyze risk of surgical resection. Multivariable Cox regression analysis was used to determine risk of postoperative complications, emergency room visits, and readmissions. Results: A total of 12,193 patients with UC and treated with disease-modifying drugs were identified. With a median follow-up time of 1.7 years, 23.8% used >1 drug, and 8.3% of patients required surgical resection. In landmark analyses, using 2 and ≥3 drugs before the landmark date was associated with higher incidence of surgery for each landmark than 1 drug. Multivariable Cox regression showed hazard ratio (95% CIs) of 4.22 (3.59-4.97), 11.7 (9.01-15.3), and 22.9 (15.0-34.9) for using 2, 3, and ≥4 drugs, respectively, compared with using 1 DMAID. That risk was constant overtime. The number of drugs used preoperatively was not associated with an increased postoperative risk of any complication, emergency room visits, or readmission. Conclusion: The use of multiple disease-modifying drugs in UC is associated with an increased risk of surgical resection with each additional drug. This provides important prognostic data and highlights the importance of patient counseling with minimal concern regarding risk of postoperative morbidity for additional drugs.
Language	English
Publishing date	2024-03-13
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2012365-6
ISSN	1873-4626 ; 1934-3213 ; 1091-255X
ISSN (online)	1873-4626 ; 1934-3213
ISSN	1091-255X
DOI	10.1016/j.gassur.2024.03.011
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Article ; Online: Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.

Deutsch, Eric W / Mendoza, Luis / Shteynberg, David D / Hoopmann, Michael R / Sun, Zhi / Eng, Jimmy K / Moritz, Robert L

Journal of proteome research

2023 Volume 22, Issue 2, Page(s) 615–624

Abstract: The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has been in continual development and refinement since its first tools, PeptideProphet and ProteinProphet, were published 20 years ago. The current release provides a large ... ...

Abstract	The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has been in continual development and refinement since its first tools, PeptideProphet and ProteinProphet, were published 20 years ago. The current release provides a large complement of tools for spectrum processing, spectrum searching, search validation, abundance computation, protein inference, and more. Many of the tools include machine-learning modeling to extract the most information from data sets and build robust statistical models to compute the probabilities that derived information is correct. Here we present the latest information on the many TPP tools, and how TPP can be deployed on various platforms from personal Windows laptops to Linux clusters and expansive cloud computing environments. We describe tutorials on how to use TPP in a variety of ways and describe synergistic projects that leverage TPP. We conclude with plans for continued development of TPP.
MeSH term(s)	Proteomics/methods ; Software ; Mass Spectrometry ; Probability ; Data Analysis
Language	English
Publishing date	2023-01-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.2c00624
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Article ; Online: Clinical research for global needs of radiation oncology.

Baumann, Michael / Bacchus, Carol / Aznar, Marianne C / Coppes, Rob P / Deutsch, Eric / Georg, Dietmar / Haustermans, Karin / Hoskin, Peter / Krause, Mechthild / Lartigau, Eric F / Lee, Anne W M / Löck, Steffen / Offersen, Birgitte V / Thwaites, David I / van der Heide, Uulke A / Valentini, Vincenzo / Overgaard, Jens

Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology

2023 Volume 190, Page(s) 110076

MeSH term(s)	Humans ; Radiation Oncology/education ; Internship and Residency ; Surveys and Questionnaires
Language	English
Publishing date	2023-12-28
Publishing country	Ireland
Document type	Editorial
ZDB-ID	605646-5
ISSN	1879-0887 ; 0167-8140
ISSN (online)	1879-0887
ISSN	0167-8140
DOI	10.1016/j.radonc.2023.110076
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Article: Mapping the

van Wijk, Klaas J / Leppert, Tami / Sun, Zhi / Kearly, Alyssa / Li, Margaret / Mendoza, Luis / Guzchenko, Isabell / Debley, Erica / Sauermann, Georgia / Routray, Pratyush / Malhotra, Sagunya / Nelson, Andrew / Sun, Qi / Deutsch, Eric W

bioRxiv : the preprint server for biology

2023

Abstract: This study describes a new release of ... ...

Abstract	This study describes a new release of the
Language	English
Publishing date	2023-06-05
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.06.01.543322
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Article ; Online: Detection of the

Journal of proteome research

2023 Volume 23, Issue 1, Page(s) 185–214

Abstract: This study describes a new release of ... ...

Abstract	This study describes a new release of the
MeSH term(s)	Humans ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Proteome/analysis ; Tandem Mass Spectrometry/methods ; Protein Processing, Post-Translational ; Peptides/analysis ; Databases, Protein
Chemical Substances	Proteome ; Peptides
Language	English
Publishing date	2023-11-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00536
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Article ; Online: Detection and editing of the updated Arabidopsis plastid- and mitochondrial-encoded proteomes through PeptideAtlas.

van Wijk, Klaas J / Bentolila, Stephane / Leppert, Tami / Sun, Qi / Sun, Zhi / Mendoza, Luis / Li, Margaret / Deutsch, Eric W

Plant physiology

2023 Volume 194, Issue 3, Page(s) 1411–1430

Abstract: Arabidopsis (Arabidopsis thaliana) ecotype Col-0 has plastid and mitochondrial genomes encoding over 100 proteins. Public databases (e.g. Araport11) have redundancy and discrepancies in gene identifiers for these organelle-encoded proteins. RNA editing ... ...

Abstract	Arabidopsis (Arabidopsis thaliana) ecotype Col-0 has plastid and mitochondrial genomes encoding over 100 proteins. Public databases (e.g. Araport11) have redundancy and discrepancies in gene identifiers for these organelle-encoded proteins. RNA editing results in changes to specific amino acid residues or creation of start and stop codons for many of these proteins, but the impact of RNA editing at the protein level is largely unexplored due to the complexities of detection. Here, we assembled the nonredundant set of identifiers, their correct protein sequences, and 452 predicted nonsynonymous editing sites of which 56 are edited at lower frequency. We then determined accumulation of edited and/or unedited proteoforms by searching ∼259 million raw tandem MS spectra from ProteomeXchange, which is part of PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/). We identified all mitochondrial proteins and all except 3 plastid-encoded proteins (NdhG/Ndh6, PsbM, and Rps16), but no proteins predicted from the 4 ORFs were identified. We suggest that Rps16 and 3 of the ORFs are pseudogenes. Detection frequencies for each edit site and type of edit (e.g. S to L/F) were determined at the protein level, cross-referenced against the metadata (e.g. tissue), and evaluated for technical detection challenges. We detected 167 predicted edit sites at the proteome level. Minor frequency sites were edited at low frequency at the protein level except for cytochrome C biogenesis 382 at residue 124 (Ccb382-124). Major frequency sites (>50% editing of RNA) only accumulated in edited form (>98% to 100% edited) at the protein level, with the exception of Rpl5-22. We conclude that RNA editing for major editing sites is required for stable protein accumulation.
MeSH term(s)	Arabidopsis/genetics ; Arabidopsis/metabolism ; Proteome/genetics ; Proteome/metabolism ; Plastids/genetics ; Plastids/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Mitochondria/genetics ; Mitochondria/metabolism
Chemical Substances	Proteome ; Arabidopsis Proteins
Language	English
Publishing date	2023-10-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1093/plphys/kiad572
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