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PIQED / Post-translational modification Identification and Quantification Exclusively from DIA

Provides a complete, automated workflow for post translational modification (PTM) identification, quantification, and statistical testing from exclusively data-independent acquisition-mass spectrometry (DIA-MS) data. PIQED is a workflow and open-source software that enables a two-fold reduction of acquisition time because both identification and quantification are achieved with a single DIA analysis. PTM-specific capabilities of this package include site localization scoring and filtering, peptide consolidation to modification site-level, and optional local or global total-ion chromatogram (TIC) normalization.


Identifies peptides from a sequence database with tandem mass spectrometry data. PEAKS employs de novo sequencing as a subroutine and exploits the de novo sequencing results to improve both the speed and accuracy of the database search. Each protein obtains a score by adding its three highest peptide CAA scores, and the protein feature of a peptide is the maximum score of the proteins containing this peptide. PEAKS also provides a user-friendly interface to show each resultant peptide spectrum match from de novo sequencing.


A MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed. InsPecT uses peptide sequence tags as efficient filters that reduce the size of the database by a few orders of magnitude while retaining the correct peptide with very high probability. In addition to filtering, InsPecT also uses novel algorithms for scoring and validating in the presence of modifications, without explicit enumeration of all variants.


Identifies unanticipated post-translational modifications (PTMs) from tandem mass spectrometry (MS/MS) data. pMatch is a dedicated open spectral library search tool that supports an entire workflow including library construction, spectral matching and result evaluation. In cooperation with traditional sequence database search, the software can push up the spectral identification rate to a large extent. Part of its advantages are the consideration of accurate mass shifts for peak matching, and the use of full peptide sequence information for consensus spectral optimization.

BioSITe / Biotinylation Site Identification Technology

Detects biotinylated peptides. BioSITe utilizes antibiotin antibodies to directly capture and find biotinylated peptides in a single liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) run. It allows for a quantitative analysis that is optimal for characterizing molecular differences across different biological conditions. This tool involves biotinylation as a strategy to tag proteins or post-translational modifications.


An algorithm that uses a large database of known PTMs to identify PTMs from MS/MS data. For a given peptide sequence, PTMTreeSearch builds a computational tree wherein each path from the root to the leaves is labeled with the amino acids of a peptide sequence. Branches then represent PTMs. Various empirical tree pruning rules have been designed to decrease the search-execution time by eliminating biologically unlikely solutions. PTMTreeSearch first identifies a relatively small set of high confidence PTM types, and in a second stage, performs a more exhaustive search on this restricted set using relaxed search parameter settings. An analysis of experimental data shows that using the same criteria for false discovery, PTMTreeSearch annotates more peptides than the current state-of-the-art methods and PTM identification algorithms, and achieves this at roughly the same execution time. PTMTreeSearch is implemented as a plugable scoring function in the X!Tandem search engine.

ProSight Lite

A free Windows application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Fixed or variable modifications, including both PTMs and a select number of glycosylations, can be applied to the amino acid sequence. The application reports multiple scores and a matching fragment list. Fragmentation maps can be exported for publication in either portable network graphic (PNG) or scalable vector graphic (SVG) format.


Matches de novo sequences to homologous proteins and overcomes many of the limitations of other sequence homology search algorithms. OpenSea was designed to align de novo sequences from all MS/MS spectra for a given experiment to database protein sequences, even in situations when de novo sequencing algorithms cannot account for an entire peptide sequence. The implementation of this algorithm can rapidly identify proteins from complex mixtures of peptides using de novo sequences derived via high mass accuracy tandem mass spectrometry.


Assists in searching in mass spectrometry-based proteomics database. Morpheus differentiates correct and incorrect identifications by counting the number of matching products in conjunction with a target-decoy approach. This software identifies protein post-translational modifications (PTM) via peptide mass spectrometry data. It exploits a two-pass database search strategy to minimize the search-pace extension but may bring biases when used with target-decoy false discovery rate calculations.

Scaffold PTM

Automates post-translational modification (PTM) site assignment in proteomic experiments. Scaffold PTM is a program assessing site assignments for any post-transnational modification (PTM). It accepts overlapping data from different peptides simultaneously to improve confidence in specific site assignments. It utilizes the Ascore algorithm to interpret sites of modification on a peptide-by-peptide basis. This tool permits users to study the peptide interpretations into protein specific sites of modification, comprised of multiple pieces of overlapping evidence.

DeltAMT / Delta Accurate Mass and Time

A statistical algorithm for fast detection of abundant protein modifications from tandem mass spectra with high-accuracy precursor masses. DeltAMT is based on the fact that the modified and unmodified versions of a peptide are usually present simultaneously in a sample and their spectra are correlated with each other in precursor masses and retention times. By representing each pair of spectra as a delta mass and time vector, bivariate Gaussian mixture models are used to detect modification-related spectral pairs.


Enables discovery and sequence mapping of modifications to target proteins known to be represented in the analysis or identified by Sequest. P-Mod matches MS/MS spectra to peptide sequences in a search list. For spectra of modified peptides, P-Mod calculates mass differences between search peptide sequences and MS/MS precursors and localizes the mass shift to a sequence position in the peptide. Because modifications are detected as mass shifts, P-Mod does not require the user to guess at masses or sequence locations of modifications. P-Mod uses extreme value statistics to assign p value estimates to sequence-to-spectrum matches. The reported p values are scaled to account for the number of comparisons, so that error rates do not increase with the expanded search lists that result from incorporating potential peptide modifications.

INKA / Integrative Inferred Kinase Activity

Serves for phosphoproteomic inference of active phosphokinases. INKA utilizes label-free quantification of phosphopeptides derived from: kinases, kinase activation loops, kinase substrates deduced from prior experimental knowledge, and kinase substrates predicted from sequence motifs. This tool is able to identify active kinases, with potential clinical significance. It combines direct observations on phosphokinases, with observations on phosphoproteins that are known or predicted substrates for the pertinent kinase.

POSTMan / POST-translational Modification analysis

Allows mass spectrometry (MS)-based identification of post-translationally modified peptides from peptide-centric datasets. POSTMan uses comparative liquid chromatography (LC)-MS datasets for identifying peptide or feature pairs present within a single chromatographic run and/or between different runs. The software can analyze any enzymatic and/or chemical manipulation of a peptide mixture that results in the addition or removal of a specific chemical moiety on a subset of peptides.


An improved workflow for identifying Ub/Ubl conjugation sites based on the ChopNSpice and X!Tandem software. ChopNSpice is modified to generate Ub/Ubl conjugation peptides in the form of a cross-link. A combinatorial FASTA database can be acquired using the modified ChopNSpice (MchopNSpice). The modified X!Tandem (UblSearch) introduces a new fragmentation model for the Ub/Ubl conjugation peptides to match unambiguously the MS/MS spectra with linear peptides or Ub/Ubl conjugation peptides using the combinatorial FASTA database. The proposed workflow is more suitable for processing large-scale MS datasets of Ub/Ubl modification.

VEMS / Virtual Expert Mass Spectrometrist

Contains a range of versatile tools for data validation and mining. VEMS performs linear recalibration of the fragments ions in a tandem Mass Spectrometry spectrum to theoretical fragment masses for each possible peptide candidate for the spectrum. It also provides an error model that validates the search results by iteratively making linear calibration. It saves search parameters and instrument settings together with spectra and the search result.


A fast and reliable method for mapping hundreds types of PTMs at a time, including novel and unexpected PTMs. The high mass accuracy of Fourier transform mass spectrometry provides in many cases unique elemental composition of the PTM through the difference DeltaM between the molecular masses of the modified and unmodified peptides, whereas the retention time difference DeltaRT between their elution in reversed-phase liquid chromatography provides an additional dimension for PTM identification.


A software tool for the automated integration of accurate intact protein mass (AIPM) and bottom-up (BU) mass spectra searches/data in order to both confidently identify the intact proteins and to characterize their post-translational modifications (PTMs). The development of PTMSearchPlus was motivated by the desire to effectively integrate high-resolution intact protein molecular masses with bottom-up peptide MS/MS data. PTMSearchPlus requires as input both intact protein and proteolytic peptide mass spectra collected from the same protein mixture, a FASTA protein database, and a selection of possible PTMs, the types and ranges of which can be specified. The output of PTMSearchPlus is a list of intact and modified proteins matching the AIPM data concomitant with their respective peptides found by the BU search. This list also contains protein and peptide sequence coverage information, scores, etc. that can be used for further evaluation or refiltering of the results.