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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
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Article ; Online: Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics.

Lu, Lei / Scalf, Mark / Shortreed, Michael R / Smith, Lloyd M

Journal of the American Society for Mass Spectrometry

2021 Volume 32, Issue 6, Page(s) 1319–1325

Abstract: Top-down proteomics is a key mass spectrometry-based technology for comprehensive analysis of proteoforms. Proteoforms exhibit multiple high charge states and isotopic forms in full MS scans. The dissociation behavior of proteoforms in different charge ... ...

Abstract	Top-down proteomics is a key mass spectrometry-based technology for comprehensive analysis of proteoforms. Proteoforms exhibit multiple high charge states and isotopic forms in full MS scans. The dissociation behavior of proteoforms in different charge states and subjected to different collision energies is highly variable. The current widely employed data-dependent acquisition (DDA) method selects a narrow
MeSH term(s)	Mass Spectrometry/methods ; Proteins/analysis ; Proteins/chemistry ; Proteomics/methods ; Saccharomyces cerevisiae Proteins/analysis ; Saccharomyces cerevisiae Proteins/chemistry ; Software
Chemical Substances	Proteins ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2021-03-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.0c00462
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Article ; Online: Towards an Ideal

Spiniello, Michele / Scalf, Mark / Casamassimi, Amelia / Abbondanza, Ciro / Smith, Lloyd M

International journal of molecular sciences

2022 Volume 23, Issue 2

Abstract: RNA-binding proteins are crucial to the function of coding and non-coding RNAs. The disruption of RNA-protein interactions is involved in many different pathological states. Several computational and experimental strategies have been developed to ... ...

Abstract	RNA-binding proteins are crucial to the function of coding and non-coding RNAs. The disruption of RNA-protein interactions is involved in many different pathological states. Several computational and experimental strategies have been developed to identify protein binders of selected RNA molecules. Amongst these, '
MeSH term(s)	Animals ; Humans ; Protein Binding ; RNA/metabolism ; RNA, Messenger/metabolism ; RNA, Untranslated/metabolism ; RNA-Binding Proteins/isolation & purification ; RNA-Binding Proteins/metabolism
Chemical Substances	RNA, Messenger ; RNA, Untranslated ; RNA-Binding Proteins ; RNA (63231-63-0)
Language	English
Publishing date	2022-01-15
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23020942
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Article ; Online: Elucidating the RNA-Protein Interactomes of Target RNAs in Tissue.

Whitworth, Isabella T / Henke, Katherine B / Yang, Bing / Scalf, Mark / Frey, Brian L / Jarrard, David F / Smith, Lloyd M

Analytical chemistry

2023 Volume 95, Issue 18, Page(s) 7087–7092

Abstract: RNA-protein interactions are key to many aspects of cellular homeostasis and their identification is important to understanding cellular function. Multiple strategies have been developed for the RNA-centric characterization of RNA-protein complexes. ... ...

Abstract	RNA-protein interactions are key to many aspects of cellular homeostasis and their identification is important to understanding cellular function. Multiple strategies have been developed for the RNA-centric characterization of RNA-protein complexes. However, these studies have all been done in immortalized cell lines that do not capture the complexity of heterogeneous tissue samples. Here, we develop hybridization purification of RNA-protein complexes followed by mass spectrometry (HyPR-MS) for use in tissue samples. We isolated both polyadenylated RNA and the specific long noncoding RNA MALAT1 and characterized their protein interactomes. These results demonstrate the feasibility of HyPR-MS in tissue for the multiplexed characterization of specific RNA-protein complexes.
MeSH term(s)	RNA, Long Noncoding/genetics ; Cell Line ; RNA, Messenger
Chemical Substances	RNA, Long Noncoding ; RNA, Messenger
Language	English
Publishing date	2023-04-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c05635
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Article ; Online: Elucidating the RNA–Protein Interactomes of Target RNAs in Tissue

Whitworth, Isabella T. / Henke, Katherine B. / Yang, Bing / Scalf, Mark / Frey, Brian L. / Jarrard, David F. / Smith, Lloyd M.

Analytical Chemistry. 2023 Apr. 24, v. 95, no. 18 p.7087-7092

2023

Abstract: RNA–protein interactions are key to many aspects of cellular homeostasis and their identification is important to understanding cellular function. Multiple strategies have been developed for the RNA-centric characterization of RNA–protein complexes. ... ...

Abstract	RNA–protein interactions are key to many aspects of cellular homeostasis and their identification is important to understanding cellular function. Multiple strategies have been developed for the RNA-centric characterization of RNA–protein complexes. However, these studies have all been done in immortalized cell lines that do not capture the complexity of heterogeneous tissue samples. Here, we develop hybridization purification of RNA–protein complexes followed by mass spectrometry (HyPR-MS) for use in tissue samples. We isolated both polyadenylated RNA and the specific long noncoding RNA MALAT1 and characterized their protein interactomes. These results demonstrate the feasibility of HyPR-MS in tissue for the multiplexed characterization of specific RNA–protein complexes.
Keywords	analytical chemistry ; homeostasis ; hybridization ; mass spectrometry ; messenger RNA ; non-coding RNA ; protein-protein interactions
Language	English
Dates of publication	2023-0424
Size	p. 7087-7092.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c05635
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Article ; Online: A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics.

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

Journal of proteome research

2020 Volume 19, Issue 5, Page(s) 1975–1981

Abstract: Statistical significance tests are a common feature in quantitative proteomics workflows. The Student' ... ...

Abstract	Statistical significance tests are a common feature in quantitative proteomics workflows. The Student's
MeSH term(s)	Bayes Theorem ; Humans ; Proteins ; Proteomics ; Software ; Workflow
Chemical Substances	Proteins
Language	English
Publishing date	2020-04-14
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.9b00796
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Article ; Online: Identifying Protein Interactomes of Target RNAs Using HyPR-MS.

Henke, Katherine B / Miller, Rachel M / Knoener, Rachel A / Scalf, Mark / Spiniello, Michele / Smith, Lloyd M

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

2021 Volume 2404, Page(s) 219–244

Abstract: RNA-protein interactions are integral to maintaining proper cellular function and homeostasis, and the disruption of key RNA-protein interactions is central to many disease states. HyPR-MS (hybridization purification of RNA-protein complexes followed by ... ...

Abstract	RNA-protein interactions are integral to maintaining proper cellular function and homeostasis, and the disruption of key RNA-protein interactions is central to many disease states. HyPR-MS (hybridization purification of RNA-protein complexes followed by mass spectrometry) is a highly versatile and efficient technology which enables multiplexed discovery of specific RNA-protein interactomes. This chapter provides extensive guidance for successful application of HyPR-MS to the system and target RNA(s) of interest, as well as a detailed description of the fundamental HyPR-MS procedure, including: (1) experimental design of controls, capture oligonucleotides, and qPCR assays; (2) formaldehyde cross-linking of cell culture; (3) cell lysis and RNA solubilization; (4) isolation of target RNA(s); (5) RNA purification and RT-qPCR analysis; (6) protein preparation and mass spectrometric analysis; and (7) mass spectrometric data analysis.
MeSH term(s)	Mass Spectrometry ; Nucleic Acid Hybridization ; Oligonucleotides ; Proteomics ; RNA/genetics
Chemical Substances	Oligonucleotides ; RNA (63231-63-0)
Language	English
Publishing date	2021-10-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1851-6_12
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Multi-step recognition of potential 5' splice sites by the

Hansen, Sarah R / White, David S / Scalf, Mark / Corrêa, Ivan R / Smith, Lloyd M / Hoskins, Aaron A

eLife

2022 Volume 11

Abstract: In eukaryotes, splice sites define the introns of pre-mRNAs and must be recognized and excised with nucleotide precision by the spliceosome to make the correct mRNA product. In one of the earliest steps of spliceosome assembly, the U1 small nuclear ... ...

Abstract	In eukaryotes, splice sites define the introns of pre-mRNAs and must be recognized and excised with nucleotide precision by the spliceosome to make the correct mRNA product. In one of the earliest steps of spliceosome assembly, the U1 small nuclear ribonucleoprotein (snRNP) recognizes the 5' splice site (5' SS) through a combination of base pairing, protein-RNA contacts, and interactions with other splicing factors. Previous studies investigating the mechanisms of 5' SS recognition have largely been done in vivo or in cellular extracts where the U1/5' SS interaction is difficult to deconvolute from the effects of
MeSH term(s)	RNA Precursors/metabolism ; RNA Splice Sites ; RNA Splicing ; Ribonucleoprotein, U1 Small Nuclear/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Spliceosomes/metabolism
Chemical Substances	RNA Precursors ; RNA Splice Sites ; Ribonucleoprotein, U1 Small Nuclear
Language	English
Publishing date	2022-08-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.70534
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Article ; Online: Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1.

Miller, Rachel M / Knoener, Rachel A / Benner, Bayleigh E / Frey, Brian L / Scalf, Mark / Shortreed, Michael R / Sherer, Nathan M / Smith, Lloyd M

Journal of proteome research

2022 Volume 21, Issue 4, Page(s) 993–1001

Abstract: Human immunodeficiency virus type 1 (HIV-1) remains a deadly infectious disease despite existing antiretroviral therapies. A comprehensive understanding of the specific mechanisms of viral infectivity remains elusive and currently limits the development ... ...

Abstract	Human immunodeficiency virus type 1 (HIV-1) remains a deadly infectious disease despite existing antiretroviral therapies. A comprehensive understanding of the specific mechanisms of viral infectivity remains elusive and currently limits the development of new and effective therapies. Through in-depth proteomic analysis of HIV-1 virions, we discovered the novel post-translational modification of highly conserved residues within the viral matrix and capsid proteins to the dehydroamino acids, dehydroalanine and dehydrobutyrine. We further confirmed their presence by labeling the reactive alkene, characteristic of dehydroamino acids, with glutathione via Michael addition. Dehydroamino acids are rare, understudied, and have been observed mainly in select bacterial and fungal species. Until now, they have not been observed in HIV proteins. We hypothesize that these residues are important in viral particle maturation and could provide valuable insight into HIV infectivity mechanisms.
MeSH term(s)	Capsid/chemistry ; Capsid/metabolism ; Capsid Proteins/analysis ; Capsid Proteins/chemistry ; Capsid Proteins/genetics ; HIV-1/genetics ; Humans ; Proteomics ; Virion
Chemical Substances	Capsid Proteins
Language	English
Publishing date	2022-02-22
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.1c00867
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Article: Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data

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

Journal of proteome research. 2020 June 25, v. 19, no. 8

2020

Abstract: Cellular functions are performed by a vast and diverse set of proteoforms. Proteoforms are the specific forms of proteins produced as a result of genetic variations, RNA splicing, and post-translational modifications (PTMs). Top-down mass spectrometric ... ...

Abstract	Cellular functions are performed by a vast and diverse set of proteoforms. Proteoforms are the specific forms of proteins produced as a result of genetic variations, RNA splicing, and post-translational modifications (PTMs). Top-down mass spectrometric analysis of intact proteins enables proteoform identification, including proteoforms derived from sequence cleavage events or harboring multiple PTMs. In contrast, bottom-up proteomics identifies peptides, which necessitates protein inference and does not yield proteoform identifications. We seek here to exploit the synergies between these two data types to improve the quality and depth of the overall proteomic analysis. To this end, we automated the large-scale integration of results from multiprotease bottom-up and top-down analyses in the software program Proteoform Suite and applied it to the analysis of proteoforms from the human Jurkat T lymphocyte cell line. We implemented the recently developed proteoform-level classification scheme for top-down tandem mass spectrometry (MS/MS) identifications in Proteoform Suite, which enables users to observe the level and type of ambiguity for each proteoform identification, including which of the ambiguous proteoform identifications are supported by bottom-up-level evidence. We used Proteoform Suite to find instances where top-down identifications aid in protein inference from bottom-up analysis and conversely where bottom-up peptide identifications aid in proteoform PTM localization. We also show the use of bottom-up data to infer proteoform candidates potentially present in the sample, allowing confirmation of such proteoform candidates by intact-mass analysis of MS1 spectra. The implementation of these capabilities in the freely available software program Proteoform Suite enables users to integrate large-scale top-down and bottom-up data sets and to utilize the synergies between them to improve and extend the proteomic analysis.
Keywords	RNA splicing ; T-lymphocytes ; automation ; cell lines ; computer software ; genetic variation ; humans ; peptides ; post-translational modification ; proteins ; proteome ; proteomics ; tandem mass spectrometry
Language	English
Dates of publication	2020-0625
Size	p. 3510-3517.
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.0c00332
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