LIVIVO - Search results -

Search results

Result 1 - 10 of total 230

Search options

Article ; Online: Proteoforms and Proteoform Families: Past, Present, and Future.

Smith, Lloyd M

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2500, Page(s) 1–4

Abstract: The Human Proteoform Project is an ambitious international effort to accelerate the development of technologies for proteoform analysis and to establish comprehensive atlases of proteoforms for humans and model organisms. Proteoforms are the ultimate ... ...

Abstract	The Human Proteoform Project is an ambitious international effort to accelerate the development of technologies for proteoform analysis and to establish comprehensive atlases of proteoforms for humans and model organisms. Proteoforms are the ultimate molecular effectors of function in biology and are thus central to understanding that function. Proteoform analysis as it is practiced today is almost exclusively accomplished by mass spectrometry (MS) and is rapidly advancing in its capabilities. This volume presents a beautiful snapshot of emerging technologies at the exciting frontier of MS-based proteoform analysis.
MeSH term(s)	Humans ; Mass Spectrometry/methods ; Protein Processing, Post-Translational ; Proteomics/methods
Language	English
Publishing date	2022-06-03
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2325-1_1
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- Full text online
- Order with fees

Article ; Online: Overview and considerations in bottom-up proteomics.

Miller, Rachel M / Smith, Lloyd M

The Analyst

2023 Volume 148, Issue 3, Page(s) 475–486

Abstract: Proteins are the key biological actors within cells, driving many biological processes integral to both healthy and diseased states. Understanding the depth of complexity represented within the proteome is crucial to our scientific understanding of ... ...

Abstract	Proteins are the key biological actors within cells, driving many biological processes integral to both healthy and diseased states. Understanding the depth of complexity represented within the proteome is crucial to our scientific understanding of cellular biology and to provide disease specific insights for clinical applications. Mass spectrometry-based proteomics is the premier method for proteome analysis, with the ability to both identify and quantify proteins. Although proteomics continues to grow as a robust field of bioanalytical chemistry, advances are still necessary to enable a more comprehensive view of the proteome. In this review, we provide a broad overview of mass spectrometry-based proteomics in general, and highlight four developing areas of bottom-up proteomics: (1) protein inference, (2) alternative proteases, (3) sample-specific databases and (4) post-translational modification discovery.
MeSH term(s)	Proteomics/methods ; Proteome/metabolism ; Protein Processing, Post-Translational ; Mass Spectrometry/methods ; Peptide Hydrolases/metabolism
Chemical Substances	Proteome ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2023-01-31
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	210747-8
ISSN	1364-5528 ; 0003-2654
ISSN (online)	1364-5528
ISSN	0003-2654
DOI	10.1039/d2an01246d
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2423: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Internal Fragment Ions Disambiguate and Increase Identifications in Top-Down Proteomics.

Rolfs, Zach / Smith, Lloyd M

Journal of proteome research

2021 Volume 20, Issue 12, Page(s) 5412–5418

Abstract: A large fraction of observed fragment ion intensity remains unidentified in top-down proteomics. The elucidation of these unknown fragment ions could enable researchers to identify additional proteoforms and reduce proteoform ambiguity in their analyses. ...

Abstract	A large fraction of observed fragment ion intensity remains unidentified in top-down proteomics. The elucidation of these unknown fragment ions could enable researchers to identify additional proteoforms and reduce proteoform ambiguity in their analyses. Internal fragment ions have received considerable attention as a major source of these unidentified fragment ions. Internal fragments are product ions that contain neither protein terminus, in contrast with terminal ions that contain a single terminus. There are many more possible internal fragments than terminal fragments, and the resulting computational complexity has historically limited the application of internal fragment ions to low-complexity samples containing only one or a few proteins of interest. We implemented internal fragment ion functionality in MetaMorpheus to allow the proteome-wide annotation of internal fragment ions. MetaMorpheus first uses terminal fragment ions to identify putative proteoforms and then employs internal fragment ions to disambiguate similar proteoforms. In the analysis of mammalian cell lysates, we found that MetaMorpheus could disambiguate over half of its previously ambiguous proteoforms while also providing up to a 7% increase in proteoform-spectrum matches identified at a 1% false discovery rate.
MeSH term(s)	Animals ; Ions ; Proteome/analysis ; Proteomics/methods
Chemical Substances	Ions ; Proteome
Language	English
Publishing date	2021-11-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00599
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6189: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Automated Assignment of Proteoform Classification Levels.

Rolfs, Zach / Smith, Lloyd M

Journal of proteome research

2021 Volume 20, Issue 8, Page(s) 4101–4105

Abstract: Proteoform identification is required to fully understand the biological diversity present in a sample. However, these identifications are often ambiguous because of the challenges in analyzing full length proteins by mass spectrometry. A five-level ... ...

Abstract	Proteoform identification is required to fully understand the biological diversity present in a sample. However, these identifications are often ambiguous because of the challenges in analyzing full length proteins by mass spectrometry. A five-level proteoform classification system was recently developed to delineate the ambiguity of proteoform identifications and to allow for comparisons across software platforms and acquisition methods. Widespread adoption of this system requires software tools to provide classification of the proteoform identifications. We describe here an implementation of the five-level classification system in the software program MetaMorpheus, which provides both bottom-up and top-down identifications. Additionally, we developed a stand-alone program called ProteoformClassifier that allows users to classify proteoform results from any search program, provided that the program writes output that includes the information necessary to evaluate proteoform ambiguity. This stand-alone program includes a small test file and database to evaluate if a given program provides sufficient information to evaluate ambiguity. If the program does not, then ProteoformClassifier provides meaningful feedback to assist developers with implementing the classification system. We tested currently available top-down software programs and found that none of them (other than MetaMorpheus) provided sufficient information regarding identification ambiguity to permit classification.
MeSH term(s)	Protein Processing, Post-Translational ; Proteome/metabolism ; Proteomics ; Software ; Tandem Mass Spectrometry
Chemical Substances	Proteome
Language	English
Publishing date	2021-06-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00417
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6189: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Spectral averaging with outlier rejection algorithms to increase identifications in top-down proteomics.

Carr, Austin V / Bollis, Nicholas E / Pavek, John G / Shortreed, Michael R / Smith, Lloyd M

Proteomics

2024 Volume 24, Issue 8, Page(s) e2300234

Abstract: The identification of proteoforms by top-down proteomics requires both high quality fragmentation spectra and the neutral mass of the proteoform from which the fragments derive. Intact proteoform spectra can be highly complex and may include multiple ... ...

Abstract	The identification of proteoforms by top-down proteomics requires both high quality fragmentation spectra and the neutral mass of the proteoform from which the fragments derive. Intact proteoform spectra can be highly complex and may include multiple overlapping proteoforms, as well as many isotopic peaks and charge states. The resulting lower signal-to-noise ratios for intact proteins complicates downstream analyses such as deconvolution. Averaging multiple scans is a common way to improve signal-to-noise, but mass spectrometry data contains artifacts unique to it that can degrade the quality of an averaged spectra. To overcome these limitations and increase signal-to-noise, we have implemented outlier rejection algorithms to remove outlier measurements efficiently and robustly in a set of MS1 scans prior to averaging. We have implemented averaging with rejection algorithms in the open-source, freely available, proteomics search engine MetaMorpheus. Herein, we report the application of the averaging with rejection algorithms to direct injection and online liquid chromatography mass spectrometry data. Averaging with rejection algorithms demonstrated a 45% increase in the number of proteoforms detected in Jurkat T cell lysate. We show that the increase is due to improved spectral quality, particularly in regions surrounding isotopic envelopes.
MeSH term(s)	Proteome/analysis ; Proteomics/methods ; Protein Processing, Post-Translational ; Algorithms ; Mass Spectrometry
Chemical Substances	Proteome
Language	English
Publishing date	2024-03-15
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202300234
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 5386: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.A 1868: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: Automated Assignment of Proteoform Classification Levels

Rolfs, Zach / Smith, Lloyd M.

Journal of proteome research. 2021 June 28, v. 20, no. 8

2021

Abstract	Proteoform identification is required to fully understand the biological diversity present in a sample. However, these identifications are often ambiguous because of the challenges in analyzing full length proteins by mass spectrometry. A five-level proteoform classification system was recently developed to delineate the ambiguity of proteoform identifications and to allow for comparisons across software platforms and acquisition methods. Widespread adoption of this system requires software tools to provide classification of the proteoform identifications. We describe here an implementation of the five-level classification system in the software program MetaMorpheus, which provides both bottom-up and top-down identifications. Additionally, we developed a stand-alone program called ProteoformClassifier that allows users to classify proteoform results from any search program, provided that the program writes output that includes the information necessary to evaluate proteoform ambiguity. This stand-alone program includes a small test file and database to evaluate if a given program provides sufficient information to evaluate ambiguity. If the program does not, then ProteoformClassifier provides meaningful feedback to assist developers with implementing the classification system. We tested currently available top-down software programs and found that none of them (other than MetaMorpheus) provided sufficient information regarding identification ambiguity to permit classification.
Keywords	automation ; biodiversity ; computer software ; databases ; mass spectrometry ; proteome ; research
Language	English
Dates of publication	2021-0628
Size	p. 4101-4105.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00417
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Cologne/Königswinter

Zs.A 6189: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: Internal Fragment Ions Disambiguate and Increase Identifications in Top-Down Proteomics

Rolfs, Zach / Smith, Lloyd M.

Journal of proteome research. 2021 Nov. 05, v. 20, no. 12

2021

Abstract	A large fraction of observed fragment ion intensity remains unidentified in top-down proteomics. The elucidation of these unknown fragment ions could enable researchers to identify additional proteoforms and reduce proteoform ambiguity in their analyses. Internal fragment ions have received considerable attention as a major source of these unidentified fragment ions. Internal fragments are product ions that contain neither protein terminus, in contrast with terminal ions that contain a single terminus. There are many more possible internal fragments than terminal fragments, and the resulting computational complexity has historically limited the application of internal fragment ions to low-complexity samples containing only one or a few proteins of interest. We implemented internal fragment ion functionality in MetaMorpheus to allow the proteome-wide annotation of internal fragment ions. MetaMorpheus first uses terminal fragment ions to identify putative proteoforms and then employs internal fragment ions to disambiguate similar proteoforms. In the analysis of mammalian cell lysates, we found that MetaMorpheus could disambiguate over half of its previously ambiguous proteoforms while also providing up to a 7% increase in proteoform-spectrum matches identified at a 1% false discovery rate.
Keywords	mammals ; proteome ; proteomics ; research
Language	English
Dates of publication	2021-1105
Size	p. 5412-5418.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00599
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Cologne/Königswinter

Zs.A 6189: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Proteoform Analysis and Construction of Proteoform Families in Proteoform Suite.

Schaffer, Leah V / Shortreed, Michael R / Smith, Lloyd M

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2500, Page(s) 67–81

Abstract: Proteoform Suite is an interactive software program for the identification and quantification of intact proteoforms from mass spectrometry data. Proteoform Suite identifies proteoforms observed by intact-mass (MS1) analysis. In intact-mass analysis, ... ...

Abstract	Proteoform Suite is an interactive software program for the identification and quantification of intact proteoforms from mass spectrometry data. Proteoform Suite identifies proteoforms observed by intact-mass (MS1) analysis. In intact-mass analysis, unfragmented experimental proteoforms are compared to a database of known proteoform sequences and to one another, searching for mass differences corresponding to well-known post-translational modifications or amino acids. Intact-mass analysis enables proteoforms observed in the MS1 data without MS/MS (MS2) fragmentation to be identified. Proteoform Suite further facilitates the construction and visualization of proteoform families, which are the sets of proteoforms derived from individual genes. Bottom-up peptide identifications and top-down (MS2) proteoform identifications can be integrated into the Proteoform Suite analysis to increase the sensitivity and accuracy of the analysis. Proteoform Suite is open source and freely available at https://github.com/smith-chem-wisc/proteoform-suite .
MeSH term(s)	Humans ; Protein Processing, Post-Translational ; Proteome/metabolism ; Proteomics/methods ; Software ; Tandem Mass Spectrometry
Chemical Substances	Proteome
Language	English
Publishing date	2022-06-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2325-1_7
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- Full text online
- Order with fees

Article ; Online: Encrypted Oligonucleotide Arrays for Molecular Authentication.

Holden, Matthew T / Smith, Lloyd M

ACS combinatorial science

2019 Volume 21, Issue 8, Page(s) 562–567

Abstract: Counterfeiting is an incredibly widespread problem, with some estimates placing its economic impact above 2% of worldwide GDP. The scale of the issue suggests that current preventive measures are either technologically insufficient or too impractical and ...

Abstract	Counterfeiting is an incredibly widespread problem, with some estimates placing its economic impact above 2% of worldwide GDP. The scale of the issue suggests that current preventive measures are either technologically insufficient or too impractical and costly to be widely adopted. High-density arrays of biomolecules are explored here as security devices that can be coupled to a valuable commodity as proof of its authenticity. Light-directed DNA array fabrication technology is used to synthesize arrays that are designed to resist analysis with sequencing-by-hybridization approaches. A relatively simple sequence design strategy forces a counterfeiter to undertake a prohibitively high number of complex experiments to decipher the array sequences employed.
MeSH term(s)	Combinatorial Chemistry Techniques ; DNA/chemical synthesis ; DNA/chemistry ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2019-07-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	2156-8944
ISSN (online)	2156-8944
DOI	10.1021/acscombsci.9b00088
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Fast, Free, and Flexible Peptide and Protein Quantification with FlashLFQ.

Millikin, Robert J / Shortreed, Michael R / Scalf, Mark / Smith, Lloyd M

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2426, Page(s) 303–313

Abstract: The rapid and accurate quantification of peptides is a critical element of modern proteomics that has become increasingly challenging as proteomic data sets grow in size and complexity. We present here FlashLFQ, a computer program for high-speed label- ... ...

Abstract	The rapid and accurate quantification of peptides is a critical element of modern proteomics that has become increasingly challenging as proteomic data sets grow in size and complexity. We present here FlashLFQ, a computer program for high-speed label-free quantification of peptides and proteins following a search of bottom-up mass spectrometry data. FlashLFQ is approximately an order of magnitude faster than established label-free quantification methods and can quantify data-dependent analysis (DDA) search results from any proteomics search program. It is available as a graphical user interface program, a command line tool, a Docker image, and integrated into the MetaMorpheus search software.
MeSH term(s)	Proteomics/methods ; Proteins/chemistry ; Peptides/chemistry ; Software ; Mass Spectrometry/methods
Chemical Substances	Proteins ; Peptides
Language	English
Publishing date	2022-11-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1967-4_13
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- Full text online
- Order with fees

To top

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED