Slater determinant

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Slater_determinant 

In quantum mechanics, a Slater determinant is an expression that describes the wave function of a multi-fermionic system. It satisfies anti-symmetry requirements, and consequently the Pauli principle, by changing sign upon exchange of two fermions. Only a small subset of all possible many-body fermionic wave functions can be written as a single Slater determinant, but those form an important and useful subset because of their simplicity.

The Slater determinant arises from the consideration of a wave function for a collection of electrons, each with a wave function known as the spin-orbital ${\displaystyle \chi (\mathbf{x})}$, where ${\displaystyle \mathbf{x}}$ denotes the position and spin of a single electron. A Slater determinant containing two electrons with the same spin orbital would correspond to a wave function that is zero everywhere.

The Slater determinant is named for John C. Slater, who introduced the determinant in 1929 as a means of ensuring the antisymmetry of a many-electron wave function, although the wave function in the determinant form first appeared independently in Heisenberg's and Dirac's articles three years earlier.

Definition

Two-particle case

The simplest way to approximate the wave function of a many-particle system is to take the product of properly chosen orthogonal wave functions of the individual particles. For the two-particle case with coordinates ${\displaystyle {\mathbf{x}}_1}$ and ${\displaystyle {\mathbf{x}}_2}$, we have

${\displaystyle \mathrm{\Psi }({\mathbf{x}}_1,{\mathbf{x}}_2)={\chi }_1({\mathbf{x}}_1){\chi }_2({\mathbf{x}}_2).}$

This expression is used in the Hartree method as an ansatz for the many-particle wave function and is known as a Hartree product. However, it is not satisfactory for fermions because the wave function above is not antisymmetric under exchange of any two of the fermions, as it must be according to the Pauli exclusion principle. An antisymmetric wave function can be mathematically described as follows:

${\displaystyle \mathrm{\Psi }({\mathbf{x}}_1,{\mathbf{x}}_2)=-\mathrm{\Psi }({\mathbf{x}}_2,{\mathbf{x}}_1).}$

This does not hold for the Hartree product, which therefore does not satisfy the Pauli principle. This problem can be overcome by taking a linear combination of both Hartree products:

${\displaystyle \begin{array}{rl}\mathrm{\Psi }({\mathbf{x}}_1,{\mathbf{x}}_2)& =\frac{1}{\sqrt{2}}\{{\chi }_1({\mathbf{x}}_1){\chi }_2({\mathbf{x}}_2)-{\chi }_1({\mathbf{x}}_2){\chi }_2({\mathbf{x}}_1)\}\\ & =\frac{1}{\sqrt{2}}\left|\begin{array}{cc}{\chi }_1({\mathbf{x}}_1)& {\chi }_2({\mathbf{x}}_1)\\ {\chi }_1({\mathbf{x}}_2)& {\chi }_2({\mathbf{x}}_2)\end{array}\right|,\end{array}}$

where the coefficient is the normalization factor. This wave function is now antisymmetric and no longer distinguishes between fermions (that is, one cannot indicate an ordinal number to a specific particle, and the indices given are interchangeable). Moreover, it also goes to zero if any two spin orbitals of two fermions are the same. This is equivalent to satisfying the Pauli exclusion principle.

Multi-particle case

The expression can be generalised to any number of fermions by writing it as a determinant. For an N-electron system, the Slater determinant is defined as

${\displaystyle \begin{array}{rl}\mathrm{\Psi }({\mathbf{x}}_1,{\mathbf{x}}_2,\dots ,{\mathbf{x}}_N)& =\frac{1}{\sqrt{N!}}\left|\begin{array}{cccc}{\chi }_1({\mathbf{x}}_1)& {\chi }_2({\mathbf{x}}_1)& \cdots & {\chi }_N({\mathbf{x}}_1)\\ {\chi }_1({\mathbf{x}}_2)& {\chi }_2({\mathbf{x}}_2)& \cdots & {\chi }_N({\mathbf{x}}_2)\\ ⋮& ⋮& \ddots & ⋮\\ {\chi }_1({\mathbf{x}}_N)& {\chi }_2({\mathbf{x}}_N)& \cdots & {\chi }_N({\mathbf{x}}_N)\end{array}\right|\\ & \equiv |{\chi }_1,{\chi }_2,\cdots ,{\chi }_N⟩\\ & \equiv |1,2,\dots ,N⟩,\end{array}}$

where the last two expressions use a shorthand for Slater determinants: The normalization constant is implied by noting the number N, and only the one-particle wavefunctions (first shorthand) or the indices for the fermion coordinates (second shorthand) are written down. All skipped labels are implied to behave in ascending sequence. The linear combination of Hartree products for the two-particle case is identical with the Slater determinant for N = 2. The use of Slater determinants ensures an antisymmetrized function at the outset. In the same way, the use of Slater determinants ensures conformity to the Pauli principle. Indeed, the Slater determinant vanishes if the set ${\displaystyle \{{\chi }_i\}}$ is linearly dependent. In particular, this is the case when two (or more) spin orbitals are the same. In chemistry one expresses this fact by stating that no two electrons with the same spin can occupy the same spatial orbital.

Example: Matrix elements in a many electron problem

See also: Slater-Condon rules

Many properties of the Slater determinant come to life with an example in a non-relativistic many electron problem.

• The one particle terms of the Hamiltonian will contribute in the same manner as for the simple Hartree product, namely the energy is summed and the states are independent
• The multi-particle terms of the Hamiltonian will introduce exchange term to lower of the energy for the anti-symmetrized wave function

Starting from a molecular Hamiltonian: $${\displaystyle {\hat{H}}_{\text{tot}}=\sum _i\frac{{\mathbf{p}}_i^2}{2m}+\sum _I\frac{{\mathbf{P}}_I^2}{2M_I}+\sum _i{V}_{\text{nucl}}({\mathbf{r}}_{\mathbf{i}})+\frac{1}{2}\sum _{i\ne j}\frac{e^2}{|{\mathbf{r}}_i-{\mathbf{r}}_j|}+\frac{1}{2}\sum _{I\ne J}\frac{Z_I{Z}_J{e}^2}{|{\mathbf{R}}_I-{\mathbf{R}}_J|}}$$ where ${\displaystyle {\mathbf{r}}_i}$ are the electrons and ${\displaystyle {\mathbf{R}}_I}$are the nuclei and

${\displaystyle V_{\text{nucl}}(\mathbf{r})=-\sum _I\frac{Z_I{e}^2}{|\mathbf{r}-{\mathbf{R}}_I|}}$

For simplicity we freeze the nuclei at equilibrium in one position and we remain with a simplified Hamiltonian

${\displaystyle {\hat{H}}_e=\sum _i^N\hat{h}({\mathbf{r}}_i)+\frac{1}{2}\sum _{i\ne j}^N\frac{e^2}{r_{ij}}}$

where

${\displaystyle \hat{h}(\mathbf{r})=\frac{{\hat{\mathbf{p}}}^2}{2m}+V_{\text{nucl}}(\mathbf{r})}$

and where we will distinguish in the Hamiltonian between the first set of terms as ${\displaystyle {\hat{G}}_1}$ (the "1" particle terms) and the last term ${\displaystyle {\hat{G}}_2}$ (the "2" particle term) which contains exchange term for a Slater determinant.

${\displaystyle {\hat{G}}_1=\sum _i^N\hat{h}({\mathbf{r}}_i)}$

${\displaystyle {\hat{G}}_2=\frac{1}{2}\sum _{i\ne j}^N\frac{e^2}{r_{ij}}}$

The two parts will behave differently when they have to interact with a Slater determinant wave function. We start to compute the expectation values of one-particle terms

${\displaystyle ⟨{\mathrm{\Psi }}_0|G_1|{\mathrm{\Psi }}_0⟩=\frac{1}{N!}⟨det\{{\psi }_1...{\psi }_N\}|G_1|det\{{\psi }_1...{\psi }_N\}⟩}$

In the above expression, we can just select the identical permutation in the determinant in the left part, since all the other N! − 1 permutations would give the same result as the selected one. We can thus cancel N! at the denominator

${\displaystyle ⟨{\mathrm{\Psi }}_0|G_1|{\mathrm{\Psi }}_0⟩=⟨{\psi }_1...{\psi }_N|G_1|det\{{\psi }_1...{\psi }_N\}⟩}$

Because of the orthonormality of spin-orbitals it is also evident that only the identical permutation survives in the determinant on the right part of the above matrix element

${\displaystyle ⟨{\mathrm{\Psi }}_0|G_1|{\mathrm{\Psi }}_0⟩=⟨{\psi }_1...{\psi }_N|G_1|{\psi }_1...{\psi }_N⟩}$

This result shows that the anti-symmetrization of the product does not have any effect for the one particle terms and it behaves as it would do in the case of the simple Hartree product.

And finally we remain with the trace over the one-particle Hamiltonians

${\displaystyle ⟨{\mathrm{\Psi }}_0|G_1|{\mathrm{\Psi }}_0⟩=\sum _i⟨{\psi }_i|h|{\psi }_i⟩}$

Which tells us that to the extent of the one-particle terms the wave functions of the electrons are independent of each other and the expectation value of total system is given by the sum of expectation value of the single particles.

For the two-particle terms instead

${\displaystyle ⟨{\mathrm{\Psi }}_0|G_2|{\mathrm{\Psi }}_0⟩=\frac{1}{N!}⟨det\{{\psi }_1...{\psi }_N\}|G_2|det\{{\psi }_1...{\psi }_N\}⟩=⟨{\psi }_1...{\psi }_N|G_2|det\{{\psi }_1...{\psi }_N\}⟩}$

If we focus on the action of one term of ${\displaystyle G_2}$, it will produce only the two terms

${\displaystyle ⟨{\psi }_1(r_1,{\sigma }_1)...{\psi }_N(r_N,{\sigma }_N)|\frac{e^2}{r_{12}}|\mathrm{d}\mathrm{e}\mathrm{t}\{{\psi }_1(r_1,{\sigma }_1)...{\psi }_N(r_N,{\sigma }_N)\}⟩=⟨{\psi }_1{\psi }_2|\frac{e^2}{r_{12}}|{\psi }_1{\psi }_2⟩-⟨{\psi }_1{\psi }_2|\frac{e^2}{r_{12}}|{\psi }_2{\psi }_1⟩}$

And finally $${\displaystyle ⟨{\mathrm{\Psi }}_0|G_2|{\mathrm{\Psi }}_0⟩=\frac{1}{2}\sum _{i\ne j}\left[⟨{\psi }_i{\psi }_j|\frac{e^2}{r_{ij}}|{\psi }_i{\psi }_j⟩-⟨{\psi }_i{\psi }_j|\frac{e^2}{r_{ij}}|{\psi }_j{\psi }_i⟩\right]}$$

which instead is a mixing term. The first contribution is called the "coulomb" term or "coulomb" integral and the second is the "exchange" term or exchange integral. Sometimes different range of index in the summation is used $\sum _{ij}$ since the Coulomb and exchange contributions exactly cancel each other for ${\displaystyle i=j}$.

It is important to notice explicitly that the exchange term, which is always positive for local spin-orbitals, is absent in the simple Hartree product. Hence the electron-electron repulsive energy ${\displaystyle ⟨{\mathrm{\Psi }}_0|G_2|{\mathrm{\Psi }}_0⟩}$ on the antisymmetrized product of spin-orbitals is always lower than the electron-electron repulsive energy on the simple Hartree product of the same spin-orbitals. Since exchange bielectronic integrals are different from zero only for spin-orbitals with parallel spins, we link the decrease in energy with the physical fact that electrons with parallel spin are kept apart in real space in Slater determinant states.

As an approximation

Most fermionic wavefunctions cannot be represented as a Slater determinant. The best Slater approximation to a given fermionic wave function can be defined to be the one that maximizes the overlap between the Slater determinant and the target wave function. The maximal overlap is a geometric measure of entanglement between the fermions.

A single Slater determinant is used as an approximation to the electronic wavefunction in Hartree–Fock theory. In more accurate theories (such as configuration interaction and MCSCF), a linear combination of Slater determinants is needed.

Discussion

The word "detor" was proposed by S. F. Boys to refer to a Slater determinant of orthonormal orbitals, but this term is rarely used.

Unlike fermions that are subject to the Pauli exclusion principle, two or more bosons can occupy the same single-particle quantum state. Wavefunctions describing systems of identical bosons are symmetric under the exchange of particles and can be expanded in terms of permanents.

Parallel evolution

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Parallel_evolution 

Parallel evolution is the similar development of a trait in distinct species that are not closely related, but share a similar original trait in response to similar evolutionary pressure.

Parallel vs. convergent evolution

Evolution at an amino acid position. In each case, the left-hand species changes from incorporating alanine (A) at a specific position within a protein in a hypothetical common ancestor deduced from comparison of sequences of several species, and now incorporates serine (S) in its present-day form. The right-hand species may undergo divergent evolution (alanine replaced with threonine instead), parallel evolution (alanine also replaced with serine), or convergent evolution (threonine replaced with serine) at this amino acid position relative to that of the first species.

Given a trait that occurs in each of two lineages descended from a specified ancestor, it is possible in theory to define parallel and convergent evolutionary trends strictly, and distinguish them clearly from one another. However, the criteria for defining convergent as opposed to parallel evolution are unclear in practice, so that arbitrary diagnosis is common. When two species share a trait, evolution is defined as parallel if the ancestors are known to have shared that similarity; if not, it is defined as convergent. However, the stated conditions are a matter of degree; all organisms share common ancestors. Scientists differ on whether the distinction is useful.

Parallel evolution between marsupials and placentals

A number of examples of parallel evolution are provided by the two main branches of the mammals, the placentals and marsupials, which have followed independent evolutionary pathways following the break-up of land-masses such as Gondwanaland roughly 100 million years ago. In South America, marsupials and placentals shared the ecosystem (before the Great American Interchange); in Australia, marsupials prevailed; and in the Old World and North America the placentals won out. However, in all these localities mammals were small and filled only limited places in the ecosystem until the mass extinction of dinosaurs sixty-five million years ago. At this time, mammals on all three landmasses began to take on a much wider variety of forms and roles. While some forms were unique to each environment, surprisingly similar animals have often emerged in two or three of the separated continents. Examples of these include the placental sabre-toothed cats (Machairodontinae) and the South American marsupial sabre-tooth (Thylacosmilus); the Tasmanian wolf and the European wolf; likewise marsupial and placental moles, flying squirrels, and (arguably) mice.

Parallel coevolution of traits between hummingbirds and sunbirds contributing to ecological guilds

Hummingbirds and sunbirds, two nectarivorous bird lineages in the New and Old Worlds have parallelly evolved a suite of specialized behavioral and anatomical traits. These traits (bill shape, digestive enzymes, and flight) allow the birds to optimally fit the flower-feeding-and-pollination ecological niche they occupy, which is shaped by the birds' suites of parallel traits. Thus, a parallel coevolved behavioral syndrome within the birds creates an emergent guild of highly specialized birds and highly adapted plants, each exploiting the other's involvement in the flowers' pollination in the Old World and New World alike.

The bill shape of nectarivores, being long and needle-like, allows them to reach down a flower's pistil/stamen and get at the nectar within. Nectarivores may also use their specialized bills to engage in nectar robbing, a practice seen in both hummingbirds and sunbirds in which the bird gets nectar by making a hole in the base of the flower's corolla tube instead of inserting its bill through the tube as is standard, thus "robbing" the flower of nectar since it is not pollinated it in return.

Nectarivores and ornithophilous flowers often exist in mutualistic guild relationships facilitated by the bird's bill shape, food source, and digestive ability acting in concert with the flower's tube shape and adaptation to pollination by hovering or perching birds. The birds eat nectar using their long, thin bills and, in so doing, collect pollen on their bills; this pollen is then transferred to the next flower they feed on. This mutualism coevolved in parallel between the Old World and New World birds and their respective flowers. Moreover, the digestive enzyme activity in nectarivores matching the nectar composition in their respective flowers appears to have coevolved in parallel between plants and pollinators across continents, as the nectarivorous lineages independently evolved the ability to digest the nectar specific to their flowers, resulting in distinct guilds.

The capacity of nectarivores to digest sucrose is far greater than that of other avian taxa. This difference is due to an analogous high concentration of sucrase-isomaltase, an enzyme that hydrolyzes sucrose. Sucrase activity per unit intestinal surface area appears to be higher in nectarivores than in other birds, meaning these nectarivorous avians can digest more sucrose more rapidly than other taxa. Moreover, the Adaptive Modulation Hypothesis does not apply for nectarivores and sugar-digesting enzymes, meaning that two lineages of nectarivores should not necessarily both have high sucrase-isomaltase concentrations even though they both eat nectar. Thus, parallel acquisition of analogous sucrose digestive capability is a reasonable conclusion because there is no apparent cause for the two lineages to share this high enzyme concentration.

Global Human Rights Defence

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Global_Human_Rights_Defence 

 

Global Human Rights Defence

Abbreviation	GHRD
Formation	2003
Type	NGO
Purpose	Welfare of minority groups, Preserving human rights
Location	The Hague, South Holland, The Netherlands
Chairman	Sradhanand Sital
Website	www.ghrd.org

Global Human Rights Defence (GHRD) is an international Non-Governmental Organization (NGO) based in The Hague, Netherlands. GHRD focuses specifically on promoting and protecting human rights worldwide. GHRD places emphasis on those areas and populations of the world where severe and extensive human rights violations of ethnic, linguistic and religious minorities have continued unabated over long periods of time, and where structural help and global attention of Governments and international institutions have failed to reach.

GHRD conducts its work via three pillars:

• Human rights reporting: done by local observers
• Humanitarian aid: aimed at victims of human rights violations
• Human rights education: in South Asia, Netherlands and Europe

Minorities

GHRD concentrates on the human rights of minority groups:

1. that are dominated by social, economical and political power;
2. that have been deprived of effective protection against gross and systematic violations;
3. that have been deprived of access to resources simply because of their identity and beliefs.

GHRD's work is based on the UN Declaration on Rights of Minorities (1992), and therefore it works with linguistic, religious and ethnic minorities.

"Basic aims of the United Nations, as proclaimed in the Charter, is to promote and encourage respect for human rights and for fundamental freedoms for all, without distinction as to race, sex, language or religion,[...] emphasizing that the constant promotion and realization of the rights of persons belonging to national or ethnic, religious and linguistic minorities, as an integral part of the development of society as a whole and within a democratic framework based on the rule of law, would contribute to the strengthening of friendship and cooperation among peoples and States" General Assembly Resolution 47/135, 18 December 1992.

Identity

GHRD is integrally distinctive from other organisations in various ways. For one, it focuses on those issues and areas where people have been deprived of their rights without their cases being properly addressed by both governments and authorities. GHRD is the first organisation in The Hague (The Netherlands) to address specifically the human rights of minorities. Outside The Hague, GHRD is distinctive because of its permanent presence of local observers, who produce genuine information and reports of distinctive quality, due to their profound knowledge of the local humanitarian situation.

Objective

GHRD has formulated the following objectives in order to fulfil its mission:

1. To fight against the violation of human rights of minority groups, particularly in those areas and populations where structural help or global attention of the world has not been given;
2. To provide refugee centre assistance and humanitarian aid to those who lack elementary basic needs such as food, clothing, shelter and proper sanitary conditions;
3. To develop, stimulate and enhance human rights awareness in a national and international perspective, through means of education.

History

GHRD was officially founded after The Hague 2003 International Conference on Human Rights, which was sub-themed Human Rights of Refugees and Victims of Ethnic and Religious Violence. At the end of the conference a gap in the human rights work was spotted: human rights of minorities. The establishment of GHRD was supported by a broad spectrum of over a 150 selected participants of national and international human rights organisations from all over the world. The memorandum of association, which was agreed upon unanimously and signed by all participating parties, provides the structure of this international organisation.

At the time of its establishment, the Board was led by Sradhanand Sital who still is the chairman of the organisation. When it was first established, GHRD had no official office and worked solely on a voluntary basis. Meetings were held at the founders’ living-rooms and activities were conducted by a small group of dedicated people. In September 2005, the organisation opened its head-office in The Hague at Javastraat and employed the first paid staff. In the building, GHRD was neighbour of United Network of Young Peacebuilders (UNOY) and United Nations High Commissioner for Refugees (UNHCR). Also in 2005, GHRD promoted a four-day congress at the City Hall of the Hague. The congress was titled GHRD reaches for the future and brought together some 120 experts in the field of human rights. Amongst the speakers were Dutch Human Rights Ambassador Mr. P. de Klerk, and the Mayor of The Hague Mr. W. Deetman.

In 2006 the founders had already some contacts in South-Asia and it was easier to start acting in the region. Moreover, the South-Asia region fulfilled the mission/vision of GHRD, as the violations of human rights of minorities did not hit the headlines nor were they on top of the political agenda.

Headquarters

GHRD head-office is based in Alexanderveld in the peace capital The Hague, South Holland, where all operations from the region are coordinated. At the time of its establishment, GHRD initially opened its offices in India, and Bangladesh. Nepal and Sri Lanka followed in 2004. Except Sri Lanka, all the offices are still active. The Sri Lanka's office had to be closed after the Tsunami in December 2004. After the disaster, a great number of NGOs started working in the country and employing local human rights experts. As a small organisation, GHRD was not able to top the salaries being paid to the locals and had to abandon the country.

In 2006, GHRD opened officially the Bhutan Chapter. GHRD had been working with the Bhutanese refugees in Nepal from the start. The observer based in Kathmandu worked closely with the seven refugee camps sponsored by the United Nations High Commission for Refugees (UNHCR). In the same year, in India the Women's Wing was launched. However, due to a lack of human resources, the division was never fully activated. GHRD has also contacts spread around Malaysia and Indonesia and is currently studying the possibility of opening an office in Pakistan. In July 2007, GHRD signed a letter of intent for exchange of information with the African foundation Bajito Onda Africa.

European Seminars

In 2006, GHRD decided to become more active in Europe and initiated a cycle of seminars on migrants in Europe and human rights. The European Seminars programme has as a basic principle the promotion of equality, unity and understanding among diverse cultures, ethnicities and religions of the world, and it seeks to create opportunities regarding peace and prosperity for mankind. Consequently, the topics tackle contemporary challenges, which cause racial enmity, social unrest and overt conflicts in all levels of society.

Seminars:

In 2006

• The Hague: Human Rights Education and Social Engagement.
• Berlin: Human Rights Education and Social Engagement—under the All Equal—All Different Campaign of the Council of Europe.

In 2007

• Turin: Intercultural Forum on Rights of Migration and Asylum (IN.F.O.R.M.A.)—under the All Different—All Equal Campaign of the Council of Europe.

In 2008

• Spain
• United Kingdom

Advocacy

Reply to Dutch Human Rights Report (2017)

In 2017, the GHRD wrote to the Dutch Ministry of Foreign affairs to criticize its recent Human Rights report. They wrote as a representative of Global Hindu Foundation (GHF) to express their objections to the report. They noted:

"We recognize that Christians are persecuted in Pakistan, as mentioned in the report, however, undue emphasis on one religion while ignoring the suffering faced by the other religious minorities could have catastrophic consequences. Religious minorities in Pakistan comprise of the Hindu, Sikh, Ahmadi communities, it is unfortunate that the Human Rights report of the Dutch Ministry of Foreign Affairs altogether disregards these minorities. The ongoing human rights violations need to cease immediately in order to ensure that religious minorities are not completely wiped out from Pakistan.

The report sadly shows the duplicity of the Dutch government in predominantly funding and supporting those organizations which work for the Christian community. The other religious minorities in Pakistan are also in dire need of international attention.

The report is built on the underlying theme that the Christian minority is the only community which faces human rights violations all over the globe. Accordingly, the Human Rights report exclusively focuses on the issues faced by members of the  Christian community."

Asia Bibi Case (2018)

GHRD staff at Mr. Malook's press briefing

On 5 November 2018, Global Human Rights Defence's (GHRD) attended the press briefing held by Mr. Saif-ul-Malook. Mr. Malook represented Asia Bibi before the Pakistan Supreme Court and has currently sought refuge in The Netherlands.

The Pakistan Supreme Court acquitted Asia Bibi of blasphemy charges citing lack of evidence on 31 October 2018. Since the judgement, Pakistan has been rocked by protests from fundamentalist groups who have made open calls for violence against the religious minorities in Pakistan. The protestors demanded that the Pakistan government must include Asia Bibi's name on the Exit Control List, in the hope that it would prevent her from flying out of the country.

Mr. Vivek, GHRD's Human Rights Officer asked him about Asia Bibi's name being put on Pakistan's Exit Control List, he replied that under the legislation, a person's name can be put onto the Exit control list only if there is a criminal case or a case of criminal fraud pending against the person. Asia Bibi does not have any pending cases against her, so her name cannot be placed on the Exit Control List. Moreover, in so far as the agreement between the government and the protesters was concerned, the agreement has no constitutional or legal validity

Mr. Malook at Asia Bibi's press conference

Kashmiri Pandits (2018)

On 1 October 2018, the GHRD sent a letter to Mr. Antonio Guterres, United Nations Secretary General, to raise the issue of the Kashmiri Pandits. They warned:

"Kashmiri Pandits, a religious minority group in the state of Jammu and Kashmir, have been systematically persecuted by the majority community since 1989. Kashmiri Pandits were forced to flee their homes and move to other parts of the country in order to save their lives, those who remained were mercilessly killed or subjected to other inhumane acts. Moreover, their religious places have been desecrated and vandalized. A brutal campaign of terror, murder, rape and arson and has been unleashed by the majority community which will stop at nothing to make sure that Kashmiri Pandits are completely wiped out from the region. There is an intentional attempt to bring about the physical destruction of the entire group."

The GHRD called for a need for the United Nations to address the situation of Kashmiri Pandits, before they are completely wiped out from the region. 

They asked for the United Nations to meet with the Global Kashmiri Pandit Diaspora (GKPD), a collective organization with members in India, USA, Australia, Canada, Singapore and Europe. It consists of volunteers who have pledged to work towards the betterment of the Kashmiri Pandit community at all levels be it political or socio-economic and cultural.

Cases

GHRD verdict on the Pabna rape case (2015)

On 13 March 2015, a 20-year-old woman belonging to the minority Hindu community was gang-raped in Pabna, Bangladesh. The victim was abducted and taken to a nearby jungle, where she was threatened with a knife and raped by the perpetrators. The perpetrators had warned her that they would kill her and her parents in case she approached the police.

The incident generated widespread attention and the case was investigated by GHRD and its local partner Research and Empowerment Organization (REO). The organizations constantly monitored the developments in the case and also provided aid to the victim and her family.

GHRD and REO identified that the authorities are not investigating the case and held protests to raise awareness about the problem. A protest was held wherein a human chain was created along with student volunteers. This pressurized the authorities to initiate action. GHRD and REO also began lobbying and advocacy efforts in Bangladesh to seek responsibility from the authorities.

After a series of protests, the police authorities finally registered the First Investigation Report (FIR) and arrested the perpetrators, Mohammed Farid Hossain (27 years) and Mohammed Hafizul (24 years). On 28 October 2018, the trial court sentenced the accused to life imprisonment. The verdict was delivered by Justice Owarul Islam.

GHRD has been also been involved in rehabilitation activities on the ground so that the victims can continue living a dignified life in society. The victim in the Pabna case has been successfully rehabilitated and is currently working with GHRD's local partner in Bangladesh, REO.

Women's Rights March in the Hague

Women's Rights March (2019)

Global Human Rights Defence (GHRD) organized an event on 7 March 2019 to highlight the persecution of religious minorities in Pakistan.

The march sought to focus international attention on the plight of minorities in Pakistan. The percentage of religious minorities in Pakistan has reduced from 23% to a mere 3.7% of the total population. Minorities are increasingly vulnerable to intimidation and attacks in Pakistan and often little is done to protect minority communities in the country.

Human Rights for Nirmala (2018)

Sukomal Bhattarai at the Nirmala event in Nepal

The GHRD helped organize a programme in Nepal for the advocacy of rights for women. Ms. Sukomal Bhattarai delivered a speech on the case of Nirmala, a 13-year-old girl who was raped and murdered. She used this case to spread a message that highlighted the prevalence of gender and religion based violence. In total 8 speeches were delivered and a panel of notables and 80 guests were present at the event.

Protest: Religious Minorities in Pakistan (2018)

GHRD organized a protest on 22 September 2018 before the United Nations in Geneva to focus international attention on the persecution of religious minorities in Pakistan.

A group of over 100 protesters participated in a march through the center of Geneva city. The protesters assembled in the city center, wearing black shirts which proclaimed “Protect Pakistani Christians”. The march began in the city center, moved past the train station and through the central business district of Geneva. The protesters then briefly halted by Lake Geneva.

The protesters helped raise awareness about the plight of Christians in Pakistan. Curious onlookers and citizens were informed about the serious violations against religious minorities in Pakistan. Specific references were made to the unjust Blasphemy laws and the Asia Bibi case. Individuals were educated about the gross violations of freedom of religion and belief, and the need for the international community to take action.

The gathering was joined by the dignitaries, Dr. Mario Silva, executive chairman of IFRAS, Mr. Henri Malosse, former president of the European Economic and Social Committee, Mr. Tomas Zdechovsky, Member of European parliament, Mr. Benjamin Blanchar, Director of SOS Chrétiens d’Orient and Mr. Gyorgy Holvenyi, Member of European Parliament.

Press Release: International Day for the Elimination of Violence against Women (2018)

GHRD protest in Geneva

On 24 November 2018, Human Rights Focus Pakistan (HRFP) in collaboration with Global Human Rights Defense (GHRD) organized an event on International Women's Day 2018 for the Elimination of Violence Against Women. The representatives of civil society organizations, women activists, political workers, social activists, HRD's, lawyers, teachers, youth and students participated to end violations against women.

The screening of the Video Documentary, “The Trapping Faiths” was also arranged during event and the all participants endorsed the recommendations jointly including to end-up the abductions, forced conversions and forced marriages of minority girls which was raised in video documentary through 4 case studies of Hindu and Christian girls, as the numbering are growing day by day. The speakers urged that state must ensure victims and their families are kept safe and all violence against women is eliminated.

Campaigns and Involvement

Stop the Gang Rapes Campaign (2007)

In 2007 GHRD started its first campaign. The initiative focused on the gang rapes that victimised Bangladeshi women and young girls. The main objective of the campaign was to raise awareness to the issue. The campaign was based in the Netherlands and it spread naturally via the internet to other European countries and even reached the United States. The campaigners used social utilities such as MySpace and Facebook to promote the message.

The campaign was also promoted via its ambassadors: Scottish band Brand New Deja Vu, DJ Paul Jay and Bangladeshi writer Taslima Nasrin. GHRD made available petitions in several languages asking the Bangladeshi government to take necessary actions. The campaign was launched on 16 June 2007 with a Beach Benefit Concert at Scheveningen (Netherlands). Performances were made by Brand New Deja Vu, DJ Paul Jay, Valerius and Little Things That Kill.

Fight Modern Slavery (2011)

In 2011, GHRD campaigned against modern slavery—existing today in forms from trafficking for the sex trade, to bonded labour, child labour, caste discrimination, and sexual exploitation. A series of activism events included: rallies, door to door campaigns, information sessions, street dramas, and screenings of the GHRD documentary. The documentary focuses specially on trafficking of girls from Nepal.

Matrix-assisted laser desorption/ionization

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https://en.wikipedia.org/wiki/Matrix-assisted_laser_desorption/ionization 

MALDI TOF mass spectrometer

In mass spectrometry, matrix-assisted laser desorption/ionization (MALDI) is an ionization technique that uses a laser energy-absorbing matrix to create ions from large molecules with minimal fragmentation. It has been applied to the analysis of biomolecules (biopolymers such as DNA, proteins, peptides and carbohydrates) and various organic molecules (such as polymers, dendrimers and other macromolecules), which tend to be fragile and fragment when ionized by more conventional ionization methods. It is similar in character to electrospray ionization (ESI) in that both techniques are relatively soft (low fragmentation) ways of obtaining ions of large molecules in the gas phase, though MALDI typically produces far fewer multi-charged ions.

MALDI methodology is a three-step process. First, the sample is mixed with a suitable matrix material and applied to a metal plate. Second, a pulsed laser irradiates the sample, triggering ablation and desorption of the sample and matrix material. Finally, the analyte molecules are ionized by being protonated or deprotonated in the hot plume of ablated gases, and then they can be accelerated into whichever mass spectrometer is used to analyse them.

History

Main article: History of mass spectrometry

The term matrix-assisted laser desorption ionization (MALDI) was coined in 1985 by Franz Hillenkamp, Michael Karas and their colleagues. These researchers found that the amino acid alanine could be ionized more easily if it was mixed with the amino acid tryptophan and irradiated with a pulsed 266 nm laser. The tryptophan was absorbing the laser energy and helping to ionize the non-absorbing alanine. Peptides up to the 2843 Da peptide melittin could be ionized when mixed with this kind of "matrix". The breakthrough for large molecule laser desorption ionization came in 1987 when Koichi Tanaka of Shimadzu Corporation and his co-workers used what they called the "ultra fine metal plus liquid matrix method" that combined 30 nm cobalt particles in glycerol with a 337 nm nitrogen laser for ionization. Using this laser and matrix combination, Tanaka was able to ionize biomolecules as large as the 34,472 Da protein carboxypeptidase-A. Tanaka received one-quarter of the 2002 Nobel Prize in Chemistry for demonstrating that, with the proper combination of laser wavelength and matrix, a protein can be ionized. Karas and Hillenkamp were subsequently able to ionize the 67 kDa protein albumin using a nicotinic acid matrix and a 266 nm laser. Further improvements were realized through the use of a 355 nm laser and the cinnamic acid derivatives ferulic acid, caffeic acid and sinapinic acid as the matrix. The availability of small and relatively inexpensive nitrogen lasers operating at 337 nm wavelength and the first commercial instruments introduced in the early 1990s brought MALDI to an increasing number of researchers. Today, mostly organic matrices are used for MALDI mass spectrometry.

Matrix

UV MALDI matrix list

Compound	Other names	Solvent	Wavelength (nm)	Applications
2,5-dihydroxy benzoic acid (gentisic acid)	DHB, gentisic acid	acetonitrile, water, methanol, acetone, chloroform	337, 355, 266	peptides, nucleotides, oligonucleotides, oligosaccharides
3,5-dimethoxy-4-hydroxycinnamic acid	sinapic acid; sinapinic acid; SA	acetonitrile, water, acetone, chloroform	337, 355, 266	peptides, proteins, lipids
4-hydroxy-3-methoxycinnamic acid	ferulic acid	acetonitrile, water, propanol	337, 355, 266	proteins
α-cyano-4-hydroxycinnamic acid	CHCA	acetonitrile, water, ethanol, acetone	337, 355	peptides, lipids, nucleotides
Picolinic acid	PA	Ethanol	266	oligonucleotides
3-hydroxy picolinic acid	HPA	Ethanol	337, 355	oligonucleotides

The matrix consists of crystallized molecules, of which the three most commonly used are sinapinic acid, α-cyano-4-hydroxycinnamic acid (α-CHCA, alpha-cyano or alpha-matrix) and 2,5-dihydroxybenzoic acid (DHB).^[16] A solution of one of these molecules is made, often in a mixture of highly purified water and an organic solvent such as acetonitrile (ACN) or ethanol. A counter ion source such as trifluoroacetic acid (TFA) is usually added to generate the [M+H] ions. A good example of a matrix-solution would be 20 mg/mL sinapinic acid in ACN:water:TFA (50:50:0.1).

Notation for cinnamic acid substitutions

The identification of suitable matrix compounds is determined to some extent by trial and error, but they are based on some specific molecular design considerations. They are of a fairly low molecular weight (to allow easy vaporization), but are large enough (with a low enough vapor pressure) not to evaporate during sample preparation or while standing in the mass spectrometer. They are often acidic, therefore act as a proton source to encourage ionization of the analyte. Basic matrices have also been reported. They have a strong optical absorption in either the UV or IR range, so that they rapidly and efficiently absorb the laser irradiation. This efficiency is commonly associated with chemical structures incorporating several conjugated double bonds, as seen in the structure of cinnamic acid. They are functionalized with polar groups, allowing their use in aqueous solutions. They typically contain a chromophore.

The matrix solution is mixed with the analyte (e.g. protein-sample). A mixture of water and organic solvent allows both hydrophobic and water-soluble (hydrophilic) molecules to dissolve into the solution. This solution is spotted onto a MALDI plate (usually a metal plate designed for this purpose). The solvents vaporize, leaving only the recrystallized matrix, but now with analyte molecules embedded into MALDI crystals. The matrix and the analyte are said to be co-crystallized. Co-crystallization is a key issue in selecting a proper matrix to obtain a good quality mass spectrum of the analyte of interest.

In analysis of biological systems, inorganic salts, which are also part of protein extracts, interfere with the ionization process. The salts can be removed by solid phase extraction or by washing the dried-droplet MALDI spots with cold water. Both methods can also remove other substances from the sample. The matrix-protein mixture is not homogeneous because the polarity difference leads to a separation of the two substances during co-crystallization. The spot diameter of the target is much larger than that of the laser, which makes it necessary to make many laser shots at different places of the target, to get the statistical average of the substance concentration within the target spot.

Naphthalene and naphthalene-like compounds can also be used as a matrix to ionize a sample.

The matrix can be used to tune the instrument to ionize the sample in different ways. As mentioned above, acid-base like reactions are often utilized to ionize the sample, however, molecules with conjugated pi systems, such as naphthalene like compounds, can also serve as an electron acceptor and thus a matrix for MALDI/TOF. This is particularly useful in studying molecules that also possess conjugated pi systems. The most widely used application for these matrices is studying porphyrin-like compounds such as chlorophyll. These matrices have been shown to have better ionization patterns that do not result in odd fragmentation patterns or complete loss of side chains. It has also been suggested that conjugated porphyrin like molecules can serve as a matrix and cleave themselves eliminating the need for a separate matrix compound.

Instrumentation

Diagram of a MALDI TOF instrument. Sample matrix ionized by radiant energy is ejected from surface. Sample travels into mass analyzer and is substantially detected.

There are several variations of the MALDI technology and comparable instruments are today produced for very different purposes, from more academic and analytical, to more industrial and high throughput. The mass spectrometry field has expanded into requiring ultrahigh resolution mass spectrometry such as the FT-ICR instruments as well as more high-throughput instruments. As many MALDI MS instruments can be bought with an interchangeable ionization source (electrospray ionization, MALDI, atmospheric pressure ionization, etc.) the technologies often overlap and many times any soft ionization method could potentially be used. For more variations of soft ionization methods see: Soft laser desorption or Ion source.

Laser

MALDI techniques typically employ the use of UV lasers such as nitrogen lasers (337 nm) and frequency-tripled and quadrupled Nd:YAG lasers (355 nm and 266 nm respectively).

Infrared laser wavelengths used for infrared MALDI include the 2.94 μm Er:YAG laser, mid-IR optical parametric oscillator, and 10.6 μm carbon dioxide laser. Although not as common, infrared lasers are used due to their softer mode of ionization. IR-MALDI also has the advantage of greater material removal (useful for biological samples), less low-mass interference, and compatibility with other matrix-free laser desorption mass spectrometry methods.

Time of flight

Sample target for a MALDI mass spectrometer

The type of a mass spectrometer most widely used with MALDI is the time-of-flight mass spectrometer (TOF), mainly due to its large mass range. The TOF measurement procedure is also ideally suited to the MALDI ionization process since the pulsed laser takes individual 'shots' rather than working in continuous operation. MALDI-TOF instruments are often equipped with a reflectron (an "ion mirror") that reflects ions using an electric field. This increases the ion flight path, thereby increasing time of flight between ions of different m/z and increasing resolution. Modern commercial reflectron TOF instruments reach a resolving power m/Δm of 50,000 FWHM (full-width half-maximum, Δm defined as the peak width at 50% of peak height) or more.

MALDI has been coupled with IMS-TOF MS to identify phosphorylated and non-phosphorylated peptides.

MALDI-FT-ICR MS has been demonstrated to be a useful technique where high resolution MALDI-MS measurements are desired.

Atmospheric pressure

Atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) is an ionization technique (ion source) that in contrast to vacuum MALDI operates at normal atmospheric environment. The main difference between vacuum MALDI and AP-MALDI is the pressure in which the ions are created. In vacuum MALDI, ions are typically produced at 10 mTorr or less while in AP-MALDI ions are formed in atmospheric pressure. In the past, the main disadvantage of the AP-MALDI technique compared to the conventional vacuum MALDI has been its limited sensitivity; however, ions can be transferred into the mass spectrometer with high efficiency and attomole detection limits have been reported. AP-MALDI is used in mass spectrometry (MS) in a variety of applications ranging from proteomics to drug discovery. Popular topics that are addressed by AP-MALDI mass spectrometry include: proteomics; mass analysis of DNA, RNA, PNA, lipids, oligosaccharides, phosphopeptides, bacteria, small molecules and synthetic polymers, similar applications as available also for vacuum MALDI instruments. The AP-MALDI ion source is easily coupled to an ion trap mass spectrometer or any other MS system equipped with electrospray ionization (ESI) or nanoESI source.

MALDI with ionization at reduced pressure is known to produce mainly singly-charged ions (see "Ionization mechanism" below). In contrast, ionization at atmospheric pressure can generate highly-charged analytes as was first shown for infrared  and later also for nitrogen lasers. Multiple charging of analytes is of great importance, because it allows to measure high-molecular-weight compounds like proteins in instruments, which provide only smaller m/z detection ranges such as quadrupoles. Besides the pressure, the composition of the matrix is important to achieve this effect.

Aerosol

In aerosol mass spectrometry, one of the ionization techniques consists in firing a laser to individual droplets. These systems are called single particle mass spectrometers (SPMS). The sample may optionally be mixed with a MALDI matrix prior to aerosolization.

Ionization mechanism

The laser is fired at the matrix crystals in the dried-droplet spot. The matrix absorbs the laser energy and it is thought that primarily the matrix is desorbed and ionized (by addition of a proton) by this event. The hot plume produced during ablation contains many species: neutral and ionized matrix molecules, protonated and deprotonated matrix molecules, matrix clusters and nanodroplets. Ablated species may participate in the ionization of analyte, though the mechanism of MALDI is still debated. The matrix is then thought to transfer protons to the analyte molecules (e.g., protein molecules), thus charging the analyte. An ion observed after this process will consist of the initial neutral molecule [M] with ions added or removed. This is called a quasimolecular ion, for example [M+H]⁺ in the case of an added proton, [M+Na]⁺ in the case of an added sodium ion, or [M-H]⁻ in the case of a removed proton. MALDI is capable of creating singly charged ions or multiply charged ions ([M+nH]ⁿ⁺) depending on the nature of the matrix, the laser intensity, and/or the voltage used. Note that these are all even-electron species. Ion signals of radical cations (photoionized molecules) can be observed, e.g., in the case of matrix molecules and other organic molecules.

The gas phase proton transfer model, implemented as the coupled physical and chemical dynamics (CPCD) model, of UV laser MALDI postulates primary and secondary processes leading to ionization. Primary processes involve initial charge separation through absorption of photons by the matrix and pooling of the energy to form matrix ion pairs. Primary ion formation occurs through absorption of a UV photon to create excited state molecules by

S₀ + hν → S₁

S₁ + S₁ → S₀ + S_n

S₁ + S_n → M⁺ + M⁻

where S₀ is the ground electronic state, S₁ the first electronic excited state, and S_n is a higher electronic excited state. The product ions can be proton transfer or electron transfer ion pairs, indicated by M⁺ and M⁻ above. Secondary processes involve ion-molecule reactions to form analyte ions.

In the lucky survivor model, positive ions can be formed from highly charged clusters produced during break-up of the matrix- and analyte-containing solid.

The lucky survivor model (cluster ionization mechanism) postulates that analyte molecules are incorporated in the matrix maintaining the charge state from solution. Ion formation occurs through charge separation upon fragmentation of laser ablated clusters. Ions that are not neutralized by recombination with photoelectrons or counter ions are the so-called lucky survivors.

The thermal model postulates that the high temperature facilitates the proton transfer between matrix and analyte in melted matrix liquid. Ion-to-neutral ratio is an important parameter to justify the theoretical model, and the mistaken citation of ion-to-neutral ratio could result in an erroneous determination of the ionization mechanism. The model quantitatively predicts the increase in total ion intensity as a function of the concentration and proton affinity of the analytes, and the ion-to-neutral ratio as a function of the laser fluences. This model also suggests that metal ion adducts (e.g., [M+Na]⁺ or [M+K]⁺) are mainly generated from the thermally induced dissolution of salt.

The matrix-assisted ionization (MAI) method uses matrix preparation similar to MALDI but does not require laser ablation to produce analyte ions of volatile or nonvolatile compounds. Simply exposing the matrix with analyte to the vacuum of the mass spectrometer creates ions with nearly identical charge states to electrospray ionization. It is suggested that there are likely mechanistic commonality between this process and MALDI.

Ion yield is typically estimated to range from 10⁻⁴ to 10⁻⁷, with some experiments hinting to even lower yields of 10⁻⁹. The issue of low ion yields had been addressed, already shortly after introduction of MALDI by various attempts, including post-ionization utilizing a second laser. Most of these attempts showed only limited success, with low signal increases. This might be attributed to the fact that axial time-of-flight instruments were used, which operate at pressures in the source region of 10⁻⁵ to 10⁻⁶, which results in rapid plume expansion with particle velocities of up to 1000 m/s. In 2015, successful laser post-ionization was reported, using a modified MALDI source operated at an elevated pressure of ~3 mbar coupled to an orthogonal time-of-flight mass analyzer, and employing a wavelength-tunable post-ionization laser, operated at wavelength from 260 nm to 280 nm, below the two-photon ionization threshold of the matrices used, which elevated ion yields of several lipids and small molecules by up to three orders of magnitude. This approach, called MALDI-2, due to the second laser, and the second MALDI-like ionization process, was afterwards adopted for other mass spectrometers, all equipped with sources operating in the low mbar range.

Applications

Biochemistry

In proteomics, MALDI is used for the rapid identification of proteins isolated by using gel electrophoresis: SDS-PAGE, size exclusion chromatography, affinity chromatography, strong/weak ion exchange, isotope coded protein labeling (ICPL), and two-dimensional gel electrophoresis. Peptide mass fingerprinting is the most popular analytical application of MALDI-TOF mass spectrometers. MALDI TOF/TOF mass spectrometers are used to reveal amino acid sequence of peptides using post-source decay or high energy collision-induced dissociation (further use see mass spectrometry).

MALDI-TOF have been used to characterise post-translational modifications. For example, it has been widely applied to study protein methylation and demethylation. However, care must be taken when studying post-translational modifications by MALDI-TOF. For example, it has been reported that loss of sialic acid has been identified in papers when dihydroxybenzoic acid (DHB) has been used as a matrix for MALDI MS analysis of glycosylated peptides. Using sinapinic acid, 4-HCCA and DHB as matrices, S. Martin studied loss of sialic acid in glycosylated peptides by metastable decay in MALDI/TOF in linear mode and reflector mode. A group at Shimadzu Corporation derivatized the sialic acid by an amidation reaction as a way to improve detection sensitivity and also demonstrated that ionic liquid matrix reduces a loss of sialic acid during MALDI/TOF MS analysis of sialylated oligosaccharides. THAP, DHAP, and a mixture of 2-aza-2-thiothymine and phenylhydrazine have been identified as matrices that could be used to minimize loss of sialic acid during MALDI MS analysis of glycosylated peptides. It has been reported that a reduction in loss of some post-translational modifications can be accomplished if IR MALDI is used instead of UV MALDI.

Besides proteins, MALDI-TOF has also been applied to study lipids. For example, it has been applied to study the catalytic reactions of phospholipases. In addition to lipids, oligonucleotides have also been characterised by MALDI-TOF. For example, in molecular biology, a mixture of 5-methoxysalicylic acid and spermine can be used as a matrix for oligonucleotides analysis in MALDI mass spectrometry, for instance after oligonucleotide synthesis.

Organic chemistry

Some synthetic macromolecules, such as catenanes and rotaxanes, dendrimers and hyperbranched polymers, and other assemblies, have molecular weights extending into the thousands or tens of thousands, where most ionization techniques have difficulty producing molecular ions. MALDI is a simple and fast analytical method that can allow chemists to rapidly analyze the results of such syntheses and verify their results.

Polymers

In polymer chemistry, MALDI can be used to determine the molar mass distribution. Polymers with polydispersity greater than 1.2 are difficult to characterize with MALDI due to the signal intensity discrimination against higher mass oligomers.

A good matrix for polymers is dithranol or AgTFA. The sample must first be mixed with dithranol and the AgTFA added afterwards; otherwise the sample will precipitate out of solution.

Microbiology

Example of a workup algorithm of possible bacterial infection in cases with no specifically requested targets (non-bacteria, mycobacteria etc.), with most common situations and agents seen in a New England community hospital setting. MALDI-TOF is seen in multiple situations in the "same day tests" row at center-bottom.

MALDI-TOF spectra are often used for the identification of microorganisms such as bacteria or fungi. A portion of a colony of the microbe in question is placed onto the sample target and overlaid with matrix. The mass spectra of expressed proteins generated are analyzed by dedicated software and compared with stored profiles for species determination in what is known as biotyping. It offers benefits to other immunological or biochemical procedures and has become a common method for species identification in clinical microbiological laboratories. Benefits of high resolution MALDI-MS performed on a Fourier transform ion cyclotron resonance mass spectrometry (also known as FT-MS) have been demonstrated for typing and subtyping viruses though single ion detection known as proteotyping, with a particular focus on influenza viruses.

One main advantage over other microbiological identification methods is its ability to rapidly and reliably identify, at low cost, a wide variety of microorganisms directly from the selective medium used to isolate them. The absence of the need to purify the suspect or "presumptive" colony allows for a much faster turn-around times. For example, it has been demonstrated that MALDI-TOF can be used to detect bacteria directly from blood cultures.

Another advantage is the potential to predict antibiotic susceptibility of bacteria. A single mass spectral peak can predict methicillin resistance of Staphylococcus aureus. MALDI can also detect carbapenemase of carbapenem-resistant enterobacteriaceae, including Acinetobacter baumannii and Klebsiella pneumoniae. However, most proteins that mediate antibiotic resistance are larger than MALDI-TOF's 2000–20,000 Da range for protein peak interpretation and only occasionally, as in the 2011 Klebsiella pneumoniae carbapenemase (KPC) outbreak at the NIH, a correlation between a peak and resistance conferring protein can be made.

Parasitology

MALDI-TOF spectra have been used for the detection and identification of various parasites such as trypanosomatids, Leishmania and Plasmodium. In addition to these unicellular parasites, MALDI/TOF can be used for the identification of parasitic insects such as lice or cercariae, the free-swimming stage of trematodes.

Medicine

MALDI-TOF spectra are often utilized in tandem with other analysis and spectroscopy techniques in the diagnosis of diseases. MALDI/TOF is a diagnostic tool with much potential because it allows for the rapid identification of proteins and changes to proteins without the cost or computing power of sequencing nor the skill or time needed to solve a crystal structure in X-ray crystallography.

One example of this is necrotizing enterocolitis (NEC), which is a devastating disease that affects the bowels of premature infants. The symptoms of NEC are very similar to those of sepsis, and many infants die awaiting diagnosis and treatment. MALDI/TOF was used to identify bacteria present in the fecal matter of NEC positive infants. This study focused on characterization of the fecal microbiota associated with NEC and did not address the mechanism of disease. There is hope that a similar technique could be used as a quick, diagnostic tool that would not require sequencing.

Another example of the diagnostic power of MALDI/TOF is in the area of cancer. Pancreatic cancer remains one of the most deadly and difficult to diagnose cancers. Impaired cellular signaling due to mutations in membrane proteins has been long suspected to contribute to pancreatic cancer. MALDI/TOF has been used to identify a membrane protein associated with pancreatic cancer and at one point may even serve as an early detection technique.

MALDI/TOF can also potentially be used to dictate treatment as well as diagnosis. MALDI/TOF serves as a method for determining the drug resistance of bacteria, especially to β-lactams (Penicillin family). The MALDI/TOF detects the presence of carbapenemases, which indicates drug resistance to standard antibiotics. It is predicted that this could serve as a method for identifying a bacterium as drug resistant in as little as three hours. This technique could help physicians decide whether to prescribe more aggressive antibiotics initially.

Detection of protein complexes

Following initial observations that some peptide-peptide complexes could survive MALDI deposition and ionization, studies of large protein complexes using MALDI-MS have been reported.

Small molecules

While MALDI is a common technique for large macro-molecules, it is often possible to also analyze small molecules with mass below 1000 Da.  The problem with small molecules is that of matrix effects, where signal interference, detector saturation, or suppression of the analyte signal is possible since the matrices often consists of small molecules themselves. The choice of matrix is highly dependent on what molecules are to be analyzed.

MALDI-imaging mass spectrometry

Due to MALDI being a soft ionization source, it is used on a wide variety of biomolecules. This has led to it being used in new ways such as MALDI-imaging mass spectrometry. This technique allows for the imaging of the spatial distribution of biomolecules.