PyFragMS─A Web Tool for the Investigation of the Collision-Induced Fragmentation Pathways

Abstract

Dissociation induced by the accumulation of internal energy via collisions of ions with neutral molecules is one of the most important fragmentation techniques in mass spectrometry (MS), and the identification of small singly charged molecules is based mainly on the consideration of the fragmentation spectrum. Many research studies have been dedicated to the creation of databases of experimentally measured tandem mass spectrometry (MS/MS) spectra (such as MzCloud, Metlin, etc.) and developing software for predicting MS/MS fragments in silico from the molecular structure (such as MetFrag, CFM-ID, CSI:FingerID, etc.). However, the fragmentation mechanisms and pathways are still not fully understood. One of the limiting obstacles is that protomers (positive ions protonated at different sites) produce different fragmentation spectra, and these spectra overlap in the case of the presence of different protomers. Here, we are proposing to use a combination of two powerful approaches: computing fragmentation trees that carry information of all consecutive fragmentations and consideration of the MS/MS data of isotopically labeled compounds. We have created PyFragMS—a web tool consisting of a database of annotated MS/MS spectra of isotopically labeled molecules (after H/D and/or 16 O/ 18 O exchange) and a collection of instruments for computing fragmentation trees for an arbitrary molecule. Using PyFragMS, we investigated how the site of protonation influences the fragmentation pathway for small molecules. Also, PyFragMS offers capabilities for performing database search when MS/MS data of the isotopically labeled compounds are taken into account.

Amine additives for improved in-ESI H/D exchange

“…For example, according to data from the recent study on the CID fragmentation pathways of deuterated molecules obtained from in-ESI H/D exchange, some molecules do not exchange amide hydrogen atoms. 13 The other groups (at least hydroxyl, carboxyl and amine groups) behaved as expected. Therefore, the extent of the in-ESI gas-phase exchange should be considered for the tasks of structure elucidation with a special focus on the compounds with amide groups.…”

“…Only the addition of DIPEA and butylamine to the deuterating solution at room temperature led to amide group H/D exchange observations. In the case of DIPEA, however, the corresponding peak, was of low intensity and poorly resolved with the 13 C peak.…”

Analysis of 16O/18O and H/D Exchange Reactions between Carbohydrates and Heavy Water Using High-Resolution Mass Spectrometry

“…It may also help in identifyingcompounds. Previously, we demonstrated how combining the isotope exchange reaction (H/D and 16 O/ 18 O)and LC-MS/MS couldhelp identify compounds in complex biological mixtures [ 24 , 25 ].…”

“…Recently, we created a PyFragMS [ 25 ] program—a web tool consisting of a database of annotated MS/MS spectra of isotopically labeled molecules (after H/D and 16 O/ 18 O exchange), instruments for investigating fragmentation pathways (creating the fragmentation tree) for arbitrary molecules, and tools for identifying unknown molecules using isotope exchange information and MS/MS data (see , accessed date: 22 February 2022). Here, we used this software to investigate the fragmentation pathway of deprotonated D-glucose by considering CID spectra after 16 O/ 18 O exchange.…”

In‐Electrospray source Hydrogen/Deuterium exchange coupled to multistage fragmentation for the investigation of the protonation and fragmentation pathways of gas phase ions

“…However, currently, there exist only two datasets of MS/MS spectra of isotopically labeled compounds: the dataset developed by Ruttkies et al and included into the MetFrag 31 and the dataset developed by our group and included into PyFragMS software. 32 Here, we are applying the in-ESI source H/D exchange reaction, MS n fragmentation, and quantum chemical calculations for the investigation of the ionization and fragmentation pathways of organic molecules. We investigated the migration of labile hydrogens from functional groups (-COOH and -NH) to the other sites of molecule during the fragmentation process and observed several unusual effects.…”