TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization

Abstract

http://proteomics.informatics.iupui.edu/software/toppic/ CONTACT: xwliu@iupui.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Single-Shot Top-Down Proteomics with Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry for Identification of Nearly 600 Escherichia coli Proteoforms

“…[31] TopFD is an improved version of MS-Deconv. [32] It converts precursor and fragment isotope clusters into monoisotopic masses and finds possible proteoform features in CZE-MS data by combining precursor isotope clusters with similar monoisotopic masses and close migration times (the isotopic clusters may have different charge states).…”

A spectrum graph-based protein sequence filtering algorithm for proteoform identification by top-down mass spectrometry

“…The Escherichia coli K-12 MG1655 proteome database (September 12, 2016 version, 4306 entries) was downloaded from the UniProt database [21] and was concatenated with a shuffled decoy database of the same size. TopPIC [6] was employed to search the deconvoluted spectra against the target-decoy database. In TopPIC, unexpected modifications were not allowed in identified proteoforms, and the error tolerances for precursor and fragment masses were set as 15 part per million (ppm).…”

“…Database search [3], [4], represented by tools such as ProSightPC [5] and TopPIC [6], is the dominant approach for top-down MS-based proteoform identification, in which top-down tandem mass (MS/MS) spectra are searched against a protein sequence database to identify matches between spectra and protein sequences. It is a challenging computational problem because the target proteoform that produced the query spectrum often contains multiple alterations that are not included in its corresponding database protein sequence.…”

“…The second approach is to employ spectral alignment algorithms [3], [4], [6], [8]–[10] to align a top-down MS/MS spectrum from a modified proteoform against unmodified database protein sequences. While spectral alignment is efficient to align a spectrum against a protein sequence, it is extremely time-consuming to align thousands of query spectra against all protein sequences in a large database.…”

De novo sequencing of proteins and peptides: algorithms, applications, perspectives

“…К популярным программам, решающим ту же задачу и находящимся в свободном доступе, относятся, относятся, например, MS-GF+ [5,6] и Andromeda [7]. В течение последнего десятилетия были также разработаны и реализованы в программных инструментах подходы к идентификации белков по данным масс-спектрометрии "сверху вниз" (top-down), анализирующие белковые молекулы целиком; наиболее широкое распространение получила коммерческая реализация ProSightPC, сопровождаемая бесплатной Интернет-версией ProSight PTM [8,9], а также свободно распространяемые MS-Align+ [10] и TopPIC [11].…”