scholarly journals Improved peptide backbone fragmentation is the primary advantage of MS-cleavable crosslinkers

2021 ◽  
Author(s):  
Lars Kolbowski ◽  
Swantje Lenz ◽  
Lutz Fischer ◽  
Ludwig R Sinn ◽  
Francis J O'Reilly ◽  
...  

Proteome-wide crosslinking mass spectrometry studies have coincided with the advent of MS-cleavable crosslinkers that can reveal the individual masses of the two crosslinked peptides. However, recently such studies have also been published with non-cleavable crosslinkers suggesting that MS-cleavability is not essential. We therefore examined in detail the advantages and disadvantages of using the most popular MS-cleavable crosslinker, DSSO. Indeed, DSSO gave rise to signature peptide fragments with a distinct mass difference (doublet) for nearly all identified crosslinked peptides. Surprisingly, we could show that it was not these peptide masses that proved the main advantage of MS-cleavability of the crosslinker, but improved peptide backbone fragmentation that allowed for more confident peptide identification. We also show that the more intricate MS3-based data acquisition approaches lack sensitivity and specificity, causing them to be outperformed by the simpler and faster stepped HCD method. This understanding will guide future developments and applications of proteome-wide crosslinking mass spectrometry.

2018 ◽  
Author(s):  
Sven H. Giese ◽  
Adam Belsom ◽  
Ludwig Sinn ◽  
Lutz Fischer ◽  
Juri Rappsilber

AbstractCrosslinking mass spectrometry draws structural information from covalently-linked peptide pairs. When these links do not match to previous structural models, they may indicate changes in protein conformation. Unfortunately, such links can also be the result of experimental error or artefacts. Here, we describe the observation of non-covalently-associated peptides during liquid chromatography-mass spectrometry analysis, which can easily be misidentified as crosslinked. Strikingly, they often mismatch to the protein structure. Non-covalently-associated peptides presumably form during ionization and can be distinguished from crosslinked peptides by observing co-elution of the corresponding linear peptides in MS1, as well as the presence of the individual (intact) peptide fragments in MS2 spectra. To suppress non-covalent peptide formations increasingly disruptive ionization settings can be used, such as in-source fragmentation.


VASA ◽  
2011 ◽  
Vol 40 (3) ◽  
pp. 188-198 ◽  
Author(s):  
Reinhold ◽  
Haage ◽  
Hollenbeck ◽  
Mickley ◽  
Ranft

In February 2008 a multidisciplinary study group was established in Germany to improve the treatment of patients with potential vascular access problems. As one of the first results of their work interdisciplinary recommendations for the management of vascular access were provided, from the creation of the initial access to the treatment of complications. As a rule the wrist arteriovenous fistula (AVF) is the access of choice due to its lower complication rate when compared to other types of access. The AVF should be created 3 months prior to the expected start of haemodialysis to allow for sufficient maturation. Second and third choice accesses are arteriovenous grafts (AVG) and central venous catheters (CVC). Ultrasound is a reliable tool for vessel selection before access creation, and also for the diagnosis of complications in AVF and grafts. Access stenosis and thrombosis can be treated surgically and interventionally. The comparison of both methods reveals advantages and disadvantages for each. The therapeutic decision should be based on the individual patients’ constitution, and also on the availability and experience of the involved specialists.


2016 ◽  
Vol 16 ◽  
pp. 179-184
Author(s):  
S. V. Kudryashova

The individual forensic activity in comparison with the activity of forensic experts of specialized state institutions is considered, the main advantages and disadvantages are determined. The directions of development of specialized state and non-state forensic institutions are presented in accordance with R. Quinn's competing values model.


Author(s):  
Piotr Szamrowski ◽  
Adam Pawlewicz

The main objective of this paper is to identify the platforms and social media tools utilized by the brewing industry in communication with the stakeholders, mainly with potential clients. In addition, the study sought to determine the nature of the published content, identify those responsible for their management, and present the advantages and disadvantages of their conduct in communication and creating the image of the company. The results indicate that only 25% of the surveyed companies do not use social media in PR. This applies only to small enterprises, with regional character. All the major brewing companies in their public relations activities use at least one type of social media, focusing in most cases on social networking (Facebook) and Video Sharing (YouTube). In addition, some of the largest brands included in the individual equity groups have their own social media channels used to communicate with the stakeholders. General promotion of company products and, what is very important, creating a dialogue with social media platform community, were seen as the most important benefits of using social media.


Author(s):  
Sunny J. Dutra ◽  
Marianne Reddan ◽  
John R. Purcell ◽  
Hillary C. Devlin ◽  
Keith M. Welker

This chapter not only draws from previous authoritative measurement overviews in the general field of emotion, but also advances these resources in several key ways. First, it provides a specific focus on positive valence systems, which have not yet received specific methodological attention. Second, the field of positive emotion (PE) has expanded in recent years with new and innovative methods, making an updated review of methodological tools timely. Third, the chapter incorporates discussion of PE disturbance in clinical populations and the methods best suited to capture PE dysfunctions. This chapter also outlines some tools that can allow researchers to capture a broad array of PE quantified by self-report, behavioral coding, and biological correlates as seen through changes in the central and peripheral nervous system (i.e., brain and body). After reviewing PE measurement methods and correlates, this chapter includes several methods for studying PE beyond the individual level (i.e., interpersonal) and traditional laboratory settings (i.e., ambulatory or experience sampling). It provides key examples of their applications to study PE in clinical populations while acknowledging several of their basic advantages and disadvantages.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Malin Indremo ◽  
Richard White ◽  
Thomas Frisell ◽  
Sven Cnattingius ◽  
Alkistis Skalkidou ◽  
...  

AbstractThe aim of this study was to examine the validity of the Gender Dysphoria (GD) diagnoses in the Swedish National Patient Register (NPR), to discuss different register-based definitions of GD and to investigate incidence trends. We collected data on all individuals with registered GD diagnoses between 2001 and 2016 as well as data on the coverage in the NPR. We regarded gender confirming medical intervention (GCMI) as one proxy for a clinically valid diagnosis and calculated the positive predictive value (PPV) for receiving GCMI for increasing number of registered GD diagnoses. We assessed crude and coverage-adjusted time trends of GD during 2004–2015 with a Poisson regression, using assigned sex and age as interaction terms. The PPV for receiving GCMI was 68% for ≥ 1 and 79% for ≥ 4 GD-diagnoses. The incidence of GD was on average 35% higher with the definition of ≥ 1 compared to the definition of ≥ 4 diagnoses. The incidence of GD, defined as ≥ 4 diagnoses increased significantly during the study period and mostly in the age categories 10–17 and 18–30 years, even after adjusting for register coverage. We concluded that the validity of a single ICD code denoting clinical GD in the Swedish NPR can be questioned. For future research, we propose to carefully weight the advantages and disadvantages of different register-based definitions according to the individual study’s needs, the time periods involved and the age-groups under study.


2021 ◽  
Author(s):  
Jifa Zhang ◽  
Yuan Jiang ◽  
Leah F Easterling ◽  
Anton Anster ◽  
Wanru Li ◽  
...  

Organosolv treatment is an efficient and environmentally friendly process to degrade lignin into small compounds. The capability of characterizing the individual compounds in the complex mixtures formed upon organosolv treatment...


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhongqi He ◽  
Christopher P. Mattison ◽  
Dunhua Zhang ◽  
Casey C. Grimm

AbstractIn this work, we sequentially extracted water (CSPw)- and alkali (CSPa)-soluble protein fractions from glandless cottonseed. SDS-Gel electrophoresis separated CSPw and CSPa to 8 and 14 dominant polypeptide bands (110–10 kDa), respectively. Liquid chromatography-electrospray ionization-tandem mass spectrometry identified peptide fragments from 336 proteins. While the majority of peptides were identified as belonging to vicilin and legumin storage proteins, peptides from other functional and uncharacterized proteins were also detected. Based on the types (unique peptide count) and relative abundance (normalized total ion current) of the polypeptides detected by mass spectrometry, we found lower levels (abundance) and types of legumin isoforms, but higher levels and more fragments of vicilin-like antimicrobial peptides in glandless samples, compared to glanded samples. Differences in peptide fragment patterns of 2S albumin and oleosin were also observed between glandless and glanded protein samples. These differences might be due to the higher extraction recovery of proteins from glandless cottonseed as proteins from glanded cottonseed tend to be associated with gossypol, reducing extraction efficiency. This work enriches the fundamental knowledge of glandless cottonseed protein composition. For practical considerations, this peptide information will be helpful to allow better understanding of the functional and physicochemical properties of glandless cottonseed protein, and improving the potential for food or feed applications.


2014 ◽  
Vol 7 (1) ◽  
pp. 3-33 ◽  
Author(s):  
F. Berthiller ◽  
P.A. Burdaspal ◽  
C. Crews ◽  
M.H. Iha ◽  
R. Krska ◽  
...  

This review highlights developments in mycotoxin analysis and sampling over a period between mid-2012 and mid-2013. It covers the major mycotoxins: aflatoxins, Alternaria toxins, ergot alkaloids, fumonisins, ochratoxins, patulin, trichothecenes and zearalenone. A wide range of analytical methods for mycotoxin determination in food and feed were developed last year, in particular immunochemical methods and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)-based methods. After a section on sampling and sample preparation, due to the rapid spread and developments in the field of LC-MS/MS multimycotoxin methods, a separate section has been devoted to this area of research. It is followed by a section on mycotoxins in botanicals and spices, before continuing with the format of previous reviews in this series with dedicated sections on method developments for the individual mycotoxins.


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