Using Statistical Models To Identify Factors That Have a Role in Defining the Abundance of Ions Produced by Tandem MS

Abstract

A database of 5448 peptide tandem mass spectra acquired in a quadrupole time-of-flight mass spectrometer was generated for peptides derived from proteins digested with trypsin. Peptides were identified from their mass spectra by the Mascot algorithm. Statistical models were then used to investigate factors influencing the abundance of ions formed. Separate models were formulated for b and y ions as it was thought that different factors may influence the formation of each type of ion. Several factors were found to have a highly significant influence on the abundance of ions formed. These include the actual mass of the ion formed after fragmentation as well as the location of the cleavage. The composition of the fragmenting peptide was also found to be important, and amino acids either side of the fragmentation site influenced the abundance of ions produced. To increase understanding of fragmentation mechanisms, the effect of several physicochemical properties of these residues was also investigated in a separate model. In conclusion, the models formulated for b and y ions provide useful characterization of the abundance of ions formed, and this information could be used to develop improved algorithms for peptide identification.

Model of ion intensity from tandem mass spectra for improved peptide identification and simulation

“…The lower the peptide charge and the lower the ion charge the higher the ion intensity which is also reported by one of the previous studies that charge state can have a dramatic effect on fragmentation of peptide [3]. B ions had significant lower intensity than the y ions (Table II), as most authors reported that y ion-series is usually more intense then b ion-series [2,3,4]. Thus, ions from non-mobile peptides, highly charged ions from highly charged peptides and b ions may not surpass the detection threshold and may not be used for accurate peptide identification.…”

“…The accuracy of the algorithms to identify peptides based on matches of the mass spectra observed to that expected based on known peptide sequence peaks is directly dependent on the precision of the spectra peaks. The fragmentation of peptide in MS/MS is a complex process and influenced by number of factors [2]. Peak intensity varies within and across ions within a peptide and the ions that do not surpass a minimum peak threshold may not be detected.…”

“…However, these attempts have been challenged by the high dimensional and multifactorial nature of the MS/MS data. For example, some studies did not consider peptide or ion charge or presence of basic amino acids in the sequence [2,3]. The goal of this study is to develop a comprehensive model that describes MS/MS intensity while accounting for multiple factors, and to offer insights into the factors that influence ion intensity.…”

Mobile protons versus mobile radicals: Gas-phase unimolecular chemistry of radical cations of cysteine-containing peptides

“…While there is still some debate on the structures of b-ions [7], the lowenergy fragmentation reactions of protonated peptides that result in the formation of both sequence and non-sequence ions are fairly well understood and have been the subject of several reviews [5][6][7][8][9][10][11]. This is due to the world-wide research efforts of many groups who have either conducted experimental and theoretical studies on small model peptides [5][6][7][8][9][10] or used statistical methods to interrogate large, curated libraries of MS/MS spectra of "real world" peptides, typically formed via tryptic digestion of proteins [12][13][14][15][16][17][18][19][20][21][22]. While more refined fragmentation models such as Paizs and Suhai's "pathways in competition (PIC)" have been developed [10], the "mobile proton" has remained center stage.…”

Charge States of y Ions in the Collision-Induced Dissociation of Doubly Charged Tryptic Peptide Ions

“…Peptide fragmentation trends derived from large collections of spectra have been published by several groups, for example [6][7][8][9][10][11], and recently reviewed [12]. Most of these studies examined the effect of specific residues, especially those adjacent to the breaking bond, and their relation to "proton mobility", on the extent of formation of specific fragments, mainly y and b ions.…”