MSQuant Free Download MSQuant is a software for MS proteomics data processing. It allows both automated and manual inspection of LC-MS data. The processed output can be a list of (scaled) peptide intensities or a list of quality scores. Source code (C++) version is available at: and binary versions (Windows and Linux) can be downloaded from: Several proteomic analyses have been carried out using MSQuant, including the identification of cisplatin induced protein, [@R54], identification of phosphorylation sites in complex samples, [@R58] and identification of plasma proteins from electrospray ionisation MS, [@R46]. The software has also been used to quantify the proteins acetylated on a single peptide, [@R11], peptide sequences, [@R30] and alternative cleavage sites of proteolysis, [@R55]. In the analysis of affinity-purified peptides and proteins, MSQuant extracts information from the MS data and applies it to predict accurate protein sequences, [@R49], [@R50]. MSQuant provides a tool to assess the quality of peptides, [@R28], [@R27], and quantify peptides and proteins in MS data. The software provides tools for quantification at the peptide, [@R57], [@R60] and protein level [@R2], [@R4]. While MSQuant processes MS runs, it can also analyse previous LC-MS runs. Using extracted data from a previous run, MSQuant can also be used to identify and quantify novel proteins, [@R12]. As well as allowing the processing of all types of MS data, MSQuant can also be used for the identification of modified peptides. For example, peptides containing phosphorylated Ser, Thr and Tyr residues can be identified using the corresponding unmodified peptide, [@R58]. We used MSQuant to analyse the data from complex samples containing multiple peptides or proteins of interest. MSQuant is ideally suited for this because it takes account of the full spectral library for each scan and is capable of analysing peptide-spectral matches (PSMs) from multiple samples. This allows it to extract meaningful information from MS data from complex samples in which it is very difficult to predict which of the proteins may be of interest. An example MSQuant For PC This uses the search results from MSQuant which it tries to interpret on a database of protein sequences. However, protein sequences are not stored in an SQL database but in a MSF format that uses a prot_seq header file. Availability: Windows binaries: GNU-linux binaries: Debian or Ubuntu Linux/Unix binaries: FreeBSD binaries: OS/X binaries: Mac OS X binaries: Source code: User Guide: - Installation - 1a423ce670 MSQuant > What's New in the? System Requirements For MSQuant: Windows 7, Windows 8 or Windows 8.1 (or newer). Windows Media Player 11 or higher. 1024x768 display, 1280x720 display or higher (1080p) CD-ROM or DVD-ROM drive (minimum of 10 Mb / s) 1024 MB of RAM 500 MB of hard drive space Non-dialup modem or broadband Internet connection (DSL, cable or other digital broadband connection) Printer. 800 × 600 screen resolution Comp
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