The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation (AI-NETD)

Riley, Nicholas M.; Rush, Matthew J. P.; Rose, Christopher M.; Richards, Alicia; Kwiecien, Nicholas W.; Bailey, Derek J.; Hebert, Alexander S.; Westphall, Michael S.; Coon, Joshua J.

doi:10.1074/mcp.m115.049726

Cited by 54 publications

(90 citation statements)

References 78 publications

(99 reference statements)

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“…Importantly, the majority of precursors sampled in negative mode nLC-MS/MS experiments are doubly deprotonated [16], suggesting the use of SF 5 •+ reagent cations could improve the depth of analysis in whole-proteome shotgun sequencing. Indeed, in 90-minute nLC-MS/MS experiments, NETD with SF 5 •+ generated 30% more PSM and unique peptide identifications than did NETD using C 16 H 10 • + (Figure 2).…”

Section: Resultsmentioning

confidence: 99%

“…Tryptic yeast ( Saccharomyces cerevisiae ) peptides were prepared as previously described[16]. Briefly, cultured yeast cells were lysed by glass bead milling (Retsch GmnH, Germany), and proteins were reduced and alkylated using 5 mM dithiothreitol and 15 mM iodoacetimide, respectively.…”

Section: Methodsmentioning

confidence: 99%

“…Inspired by McLuckey’s experiment, we developed ion-ion reaction chemistries to abstract electrons from multiply deprotonated peptide anions using singly charged reagent cations, termed negative electron transfer dissociation (NETD) [11]. NETD has emerged as one of the most promising peptide anion dissociation methods and has been successfully utilized in nLC-MS/MS experiments to access the acidic proteome[11, 12, 16, 17, 30]. …”

Section: Introductionmentioning

confidence: 99%

“…The additional energy can disrupt the non-covalent interactions holding these ions together, yielding sequence informative products[40, 41]. One such approach, termed activated-ion NETD (AI-NETD), has been implemented by concurrently irradiating the ions with infrared photons as they are interacting; however, this approach requires the addition of an IR laser to the system[16, 30]. …”

Section: Introductionmentioning

confidence: 99%

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Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation

Rush

Riley

Westphall³

et al. 2017

J. Am. Soc. Mass Spectrom.

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Negative mode proteome analysis offers access to unique portions of the proteome and several acidic post-translational modifications; however, traditional collision-based fragmentation methods fail to reliably provide sequence information for peptide anions. Negative electron transfer dissociation (NETD), on the other hand, can sequence precursor anions in a high-throughput manner. Similar to other ion-ion methods, NETD is most efficient with peptides of higher charge state due to the increased electrostatic interaction between reacting molecules. Here we demonstrate that NETD performance for lower charge state precursors can be improved by altering the reagent cation. Specifically, the recombination energy of the NETD reaction–largely dictated by the ionization energy (IE) of the reagent cation–can affect the extent of fragmentation. We compare the NETD reagent cations of C16H10•+ (IE = 7.9 eV) and SF5•+ (IE = 9.6 eV) on a set of standard peptides, concluding that SF5•+ yields greater sequence ion generation. Subsequent proteome-scale nLC-MS/MS experiments comparing C16H10•+ and SF5•+ further supported this outcome: analyses using SF5•+ yielded 4,637 peptide spectral matches (PSMs) and 2,900 unique peptides, whereas C16H10•+ produced 3,563 PSMs and 2,231 peptides. The substantive gain in identification power with SF5•+ was largely driven by improved identification of doubly deprotonated precursors, indicating that increased NETD recombination energy can increase product ion yield for low charge density precursors. This work demonstrates that SF5•+ is a viable, if not favorable, reagent cation for NETD, and provides improved fragmentation over the commonly used fluoranthene reagent.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation

Rush

Riley

Westphall³

et al. 2017

J. Am. Soc. Mass Spectrom.

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“…27–31 Coon and co-workers demonstrated the use of alkaline separations and negative ion mode detection as an effective method to probe the acidic proteome. 23,32 However, in contrast to positive ion mode, nESI unfortunately does not typically perform robustly in negative ion mode.…”

Section: Introductionmentioning

confidence: 99%

Corona Discharge Suppression in Negative Ion Mode Nanoelectrospray Ionization via Trifluoroethanol Addition

McClory

Håkansson

2017

Anal. Chem.

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Negative ion mode nanoelectrospray ionization (nESI) is often utilized to analyze acidic compounds, from small molecules to proteins, with mass spectrometry (MS). Under high aqueous solvent conditions corona discharge is commonly observed at emitter tips, resulting in low ion abundances and reduced nESI needle lifetimes. We have successfully reduced corona discharge in negative ion mode by trace addition of trifluoroethanol (TFE) to aqueous samples. The addition of as little as 0.2% TFE increases aqueous spray stability not only in nESI direct infusion, but also in nanoflow liquid chromatography (nLC)/MS experiments. Negative ion mode spray stability with 0.2% TFE is approximately six times higher than for strictly aqueous samples. Upon addition of 0.2% TFE to the mobile phase of nLC/MS experiments, tryptic peptide identifications increased from 93 to 111 peptides, resulting in an average protein sequence coverage increase of 18%.

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Photodissociation Mass Spectrometry of Peptides and Proteins

Julia¹,

Oliveira²

2018

Encyclopedia of Analytical Chemistry

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Photodissociation has been extensively explored in the last decades for the analysis of peptides and proteins by mass spectrometry (MS). In the photodissociation process, ions interact with photons generating an increment on internal energy that leads to their fragmentation. The specific characteristics of photodissociation techniques have led to improvements in different applications of MS. Among them, the cleavage of molecular bonds in a selective manner, based on the incorporation of chromophore molecules. Moreover, the ability to generate an almost complete array of fragment ions is the main reason for the increment in the utilization of ultraviolet photodissociation (UVPD). This technique has been applied to the most challenging proteomics studies, such as the characterization of posttranslational modifications and protein sequence variations, de novo sequencing, and the analysis of intact proteins. This article is focused on the most recent and relevant developments of infrared photodissociation and UVPD techniques and their application to the study of peptides and proteins.

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The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation (AI-NETD)

Cited by 54 publications

References 78 publications

Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation

Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation

Corona Discharge Suppression in Negative Ion Mode Nanoelectrospray Ionization via Trifluoroethanol Addition

Photodissociation Mass Spectrometry of Peptides and Proteins

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