Mass-spectrometry-based proteomics has become an important component of biological research. Numerous proteomics methods have been developed to identify and quantify the proteins in biological and clinical samples1, identify pathways affected by endogenous and exogenous perturbations2, and characterize protein complexes3. Despite successes, the interpretation of vast proteomics datasets remains a challenge. There have been several calls for improvements and standardization of proteomics data analysis frameworks, as well as for an application-programming interface for proteomics data access4,5. In response, we have developed the ProteoWizard Toolkit, a robust set of open-source, software libraries and applications designed to facilitate proteomics research. The libraries implement the first-ever, non-commercial, unified data access interface for proteomics, bridging field-standard open formats and all common vendor formats. In addition, diverse software classes enable rapid development of vendor-agnostic proteomics software. Additionally, ProteoWizard projects and applications, building upon the core libraries, are becoming standard tools for enabling significant proteomics inquiries.

Summary: The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library.Availability: Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.Contact: darren@proteowizard.org; parag@ucla.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Since 1969 t h e Canadian Hydrographic Service has been active in the development of a semiautomated hydrographic survey system. The Hydrographic Acquisition and Processing System (HAAE'S) employs hard-wired data loggers weighi n g 66 kilograms and having a power requirement of 350 w a t t s at 24 v o l t s d . c . I n s t a l l e d i n 7.6-metre survey launches, t h e d a t a l o g g e r s a r e used t o r e c o r d d i g i t a l d e p t h and p o s i t i o n d a t a on magnetic tape. A computer f a c i l i t y is carr i e d on t h e mother s h i p . Depth d a t a a r e e d i t e d by t h e computer t o r e t a i n t h e deeps and shallows r e q u i r e d t o d e l i n e a t e t h e t o p o g r a p h y . The c r i t e r i o n i s s u c h t h a t o v e r p r i n t i n g does n o t occur when t h e s e l e c t e d d e p t h s a r e p l o t t e d . Processed data w i l l be eventually used as t h e i n p u t t o an automated cartographic system. INTRGDUCTION The fundamental role o f the hydrographer i s t h e simultaneous measurement of two parameters, d e p t h a n d p o s i t i o n . I n r e c e n t y e a r s t h e r e have been a c c e l e r a t e d e f f o r t s by many c o u n t r i e s towards the automation of hydrography. Y 2 I n t eg r a t e d c i r c u i t s a n d mini-computers have c r e a t e d many new p o s s i b i l i t i e s f o r t h o s e c o n c e r n e d w i t h t h e c o l l e c t i o n a n d p r o c e s s i n g o f s u r v e y d a t a . This paper gives a b r i e f o u t l i n e o f t h e Hydrographic Acquisition and Processing System (HAAPS) used by t h e Canadian Hydrographic Service. The o f f -l i n e , hard-wired data loggers , t h e computer f a c i l i t y a n d t h e p r o c e s s i n g o f d a t a a r e d e s c r i b e d . DATA ACQUISITIONThe semi-automated survey system as implemented by t h e Canadian Hydrographic Service employs hard-wired data loggers, weighing approximately 66 kilograms and having a power requirement of 350 watts at 24 volts d.c.The mother s h i p a n d t h e 7 . 6 metre survey launches are each equipped with a logging system. Sounding lines a r e s p a c e d i n a c c o r d a n c e w i t h t h e c r i t e r i a o f conventional hydrography. Figure 1 shows t h e t y p e of launch used with this system. A small computing f a c i l i t y i s i n s t a l l e d on t h e mother s h i p , o r i n t h e s h o r e -b a s e d h e a d q u a r t e r s , f o r d a t a p r o c e s s i n g . All d a t a a c q u i s i t i o n i s independent of t h e computing system m d subsequent processing i s done i n a batch mode. The main components o f t h e d a t a l o g g i n g system are (see Fipure 2 ) :1. 2.3. AnA model 10251 Digital Control Unit (DCU) manufactured by Decca Survey Systems Inc. It i s u s e d a s t h e c o n t r o l l e r . The DCU cont a i n s a clock, a d i g i t i z e r for t h e e l e c t r o n i c positioning system and sequencing circuits t o scan and format data for magnetic tape. A Kennedy Model 1600 Write-Only D i g i t a l Incremental Recorder. A l l d a ...